Programs launching from top on occasions when being unminimized from bottom

I am running Ubuntu Gnome 15.04, with Gnome Shell, and ever since I upgraded to Gnome 3.16 from 3.14 I have noticed that when unminimizing something from Docky, if I click on the icon the first time it will normally come up, but when I minimize it again, and then unminimize it the same way (although this isn't always necessary and it may do it the first time, for better results and a greater chance of reproducing it, you should try this many times), instead of it doing its cool opening from the bottom where the icon is (as Docky is docked to the bottom of my screen) it opens the same, but from the top of my screen, as if Docky was at the top and not the bottom, but I am certain of it that it is at the bottom for I can see it there with my own eyes.

I ran Docky with the debugging option, and reproduced the bug, and this was the output:

[Info 13:10:41.846] Docky version: 2.2.0 Release
[Info 13:10:41.948] Kernel version: 3.19.0.25
[Info 13:10:41.956] CLR version: 4.0.30319.17020
[Debug 13:10:42.900] [UserArgs] BufferTime = 0
[Debug 13:10:42.900] [UserArgs] MaxSize = 2147483647
[Debug 13:10:42.901] [UserArgs] NetbookMode = False
[Debug 13:10:42.901] [UserArgs] NoPollCursor = False
[Error 13:10:42.947] [SystemService] Could not initialize power manager dbus: 'org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.UPower" doesn't exist
'
[Info 13:10:42.951] [SystemService] at Docky.Services.SystemService+IUPowerProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at Docky.Services.SystemService.HandleUPowerChanged () [0x00000] in <filename unknown>:0
  at Docky.Services.SystemService.InitializeBattery () [0x00000] in <filename unknown>:0
[Info 13:10:43.013] [ThemeService] Setting theme: HUD
[Debug 13:10:43.106] [DesktopItemService] Loading remap file '/usr/share/docky/remaps.ini'.
[Debug 13:10:43.147] [DesktopItemService] Remapping 'Picasa3.exe' to 'picasa'.
[Debug 13:10:43.147] [DesktopItemService] Remapping 'nbexec' to 'netbeans'.
[Debug 13:10:43.147] [DesktopItemService] Remapping 'deja-dup-preferences' to 'deja-dup'.
[Debug 13:10:43.147] [DesktopItemService] Remapping 'VirtualBox' to 'virtualbox'.
[Warn 13:10:43.148] [DesktopItemService] Could not find remap file '/home/arthur-dent/.local/share/docky/remaps.ini'!
[Debug 13:10:43.152] [DesktopItemService] Loading desktop item cache '/home/arthur-dent/.cache/docky/docky.desktop.en_GB.UTF-8.cache'.
[Info 13:10:43.436] [DockServices] Dock services initialized.
[Debug 13:10:43.494] [DBusManager] DBus Registered: org.gnome.Docky
[Debug 13:10:43.532] [DBusManager] DBus Registered: net.launchpad.DockManager
[Debug 13:10:44.356] [PluginManager] Plugin manager initialized.
[Debug 13:10:44.387] [PluginManager] Processing config file for "Battery Monitor".
[Debug 13:10:44.401] [PluginManager] Processing config file for "Bookmarks".
[Debug 13:10:44.401] [PluginManager] Processing config file for "CPU Monitor".
[Debug 13:10:44.402] [PluginManager] Processing config file for "Clippy".
[Debug 13:10:44.403] [PluginManager] Processing config file for "Clock".
[Debug 13:10:44.403] [PluginManager] Processing config file for "Desktop".
[Debug 13:10:44.404] [PluginManager] Processing config file for "Gmail".
[Debug 13:10:44.405] [PluginManager] Processing config file for "Mounter".
[Debug 13:10:44.406] [PluginManager] Processing config file for "NPR".
[Debug 13:10:44.431] [PluginManager] Processing config file for "Network Manager".
[Debug 13:10:44.431] [PluginManager] Processing config file for "Network Monitor".
[Debug 13:10:44.432] [PluginManager] Processing config file for "Recent Documents".
[Debug 13:10:44.433] [PluginManager] Processing config file for "Session Manager".
[Debug 13:10:44.434] [PluginManager] Processing config file for "Timer".
[Debug 13:10:44.435] [PluginManager] Processing config file for "Trash".
[Debug 13:10:44.436] [PluginManager] Processing config file for "Weather".
[Debug 13:10:44.436] [PluginManager] Processing config file for "Workspace Switcher".
[Info 13:10:44.781] [PluginManager] Loaded "Mounter".
[Info 13:10:44.781] [PluginManager] Loaded "Trash".
[Info 13:10:44.831] [PluginManager] Loaded "Network Manager".
[Info 13:10:44.831] [PluginManager] Loaded "Battery Monitor".
[Debug 13:10:44.869] [BatteryMonitorProcItem] Hiding battery item (capacity=0) (max_capacity=-1) (OnBattery=False)
[Info 13:10:44.870] [PluginManager] Loaded "CPU Monitor".
[Error 13:10:45.008] [ConnectionManager] Object reference not set to an instance of an object
[Debug 13:10:45.008] [ConnectionManager] at NetworkManagerDocklet.ConnectionManager.UpdateConnections () [0x00000] in <filename unknown>:0
[Error 13:10:45.008] [ConnectionManager] Object reference not set to an instance of an object
[Debug 13:10:45.008] [ConnectionManager] at NetworkManagerDocklet.ConnectionManager.UpdateConnections () [0x00000] in <filename unknown>:0
[Error 13:10:45.025] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.026] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.028] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.028] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.030] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.030] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.059] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.059] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.061] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.061] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.063] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.064] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.066] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.067] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.068] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.068] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.071] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.071] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_DType () [0x00000] in <filename unknown>:0
[Error 13:10:45.077] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.077] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.078] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.078] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.104] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.105] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.106] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.106] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.107] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.107] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.108] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.108] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.109] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.109] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.110] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.110] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:45.111] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:45.111] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Info 13:10:45.120] [PluginManager] Loaded "Network Monitor".
[Info 13:10:45.761] [HelperService] Helper added: /usr/share/dockmanager/scripts/banshee_control.py
[Info 13:10:45.762] [HelperService] Helper added: /usr/share/dockmanager/scripts/deluge_badge.py
[Info 13:10:45.762] [HelperService] Helper added: /usr/share/dockmanager/scripts/emesene_control.py
[Info 13:10:45.763] [HelperService] Helper added: /usr/share/dockmanager/scripts/gajim_badge.py
[Info 13:10:45.763] [HelperService] Helper added: /usr/share/dockmanager/scripts/gtg_menus.py
[Info 13:10:45.763] [HelperService] Helper added: /usr/share/dockmanager/scripts/liferea_badge.py
[Info 13:10:45.763] [HelperService] Helper added: /usr/share/dockmanager/scripts/mpd_control.py
[Info 13:10:45.764] [HelperService] Helper added: /usr/share/dockmanager/scripts/open_terminal_here.py
[Info 13:10:45.764] [HelperService] Helper added: /usr/share/dockmanager/scripts/pidgin_control.py
[Info 13:10:45.764] [HelperService] Helper added: /usr/share/dockmanager/scripts/pithos_control.py
[Info 13:10:45.764] [HelperService] Helper added: /usr/share/dockmanager/scripts/rhythmbox_control.py
[Info 13:10:45.765] [HelperService] Helper added: /usr/share/dockmanager/scripts/skype_control.py
[Info 13:10:45.765] [HelperService] Helper added: /usr/share/dockmanager/scripts/tomboy_menus.py
[Info 13:10:45.765] [HelperService] Helper added: /usr/share/dockmanager/scripts/transmission_badge.py
[Info 13:10:45.765] [HelperService] Helper added: /usr/share/dockmanager/scripts/tsclient_menus.py
[Info 13:10:45.766] [HelperService] Helper added: /usr/share/dockmanager/scripts/workrave_helper.py
[Info 13:10:45.766] [HelperService] Helper added: /usr/share/dockmanager/scripts/zeitgeist_journal.py
[Info 13:10:45.766] [HelperService] Helper added: /usr/share/dockmanager/scripts/zeitgeist_menus.py
[Warn 13:10:46.064] [DrawingService] Error loading icon from file '/usr/share/pithos/media/icon.svg': Failed to open file '/usr/share/pithos/media/icon.svg': No such file or directory
[Debug 13:10:46.065] [DrawingService] at Gdk.Pixbuf..ctor (System.String filename, Int32 width, Int32 height, Boolean preserve_aspect_ratio) [0x00000] in <filename unknown>:0
  at Docky.Services.DrawingService.IconFromFile (System.String name, Int32 width, Int32 height) [0x00000] in <filename unknown>:0
[Info 13:10:46.069] [DrawingService] Could not find '/usr/share/pithos/media/icon.svg', using fallback of 'extension'.
[Warn 13:10:46.163] [DrawingService] Error loading icon from file '/usr/share/pixmaps/workrave/workrave.xpm': Failed to open file '/usr/share/pixmaps/workrave/workrave.xpm': No such file or directory
[Debug 13:10:46.163] [DrawingService] at Gdk.Pixbuf..ctor (System.String filename, Int32 width, Int32 height, Boolean preserve_aspect_ratio) [0x00000] in <filename unknown>:0
  at Docky.Services.DrawingService.IconFromFile (System.String name, Int32 width, Int32 height) [0x00000] in <filename unknown>:0
[Info 13:10:46.163] [DrawingService] Could not find '/usr/share/pixmaps/workrave/workrave.xpm', using fallback of 'extension'.
[Info 13:10:46.472] [DrawingService] Could not find 'network-wireless-connected-75', using fallback of 'gnome-netstatus-75-100'.
Cairo.Surface is leaking, programmer is missing a call to Dispose
Set MONO_CAIRO_DEBUG_DISPOSE to track allocation traces
[Info 13:10:46.783] [DrawingService] Could not find 'network-wireless-connected-75', using fallback of 'gnome-netstatus-75-100'.
[Error 13:10:55.138] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.138] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.139] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.139] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.140] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.140] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.142] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.142] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.143] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.143] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.144] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.144] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.145] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.145] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.146] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.146] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Error 13:10:55.146] [NetworkDevice] org.freedesktop.DBus.Error.UnknownMethod: Method "Get" with signature "ss" on interface "org.freedesktop.NetworkManager.Device" doesn't exist

[Debug 13:10:55.146] [NetworkDevice] at NetworkManagerDocklet.INetworkDeviceProxy.Get (System.String interface, System.String propname) [0x00000] in <filename unknown>:0
  at NetworkManagerDocklet.NetworkDevice.get_State () [0x00000] in <filename unknown>:0
[Info 13:10:55.151] [DrawingService] Could not find 'network-wireless-connected-75', using fallback of 'gnome-netstatus-75-100'.

---

OS Information:

    No LSB modules are available.
    Distributor ID: Ubuntu
    Description: Ubuntu 15.04
    Release: 15.04
    Codename: vivid

Package Information:

    docky:
      Installed: 2.2.0-2
      Candidate: 2.2.0-2
      Version table:
     *** 2.2.0-2 0
            500 http://gb.archive.ubuntu.com/ubuntu/ vivid/universe amd64 Packages
            100 /var/lib/dpkg/status