I have two monitors, via the Nvidia driver and TwinView, and it seems to be impossible to drag docky from any position to the bottom of the right monitor.
This may be related to the monitors being in different resolutions - the left is 1680x1050 and the right is 1280x1024. Interestingly I can open up gconf-editor and change the monitor number, or the position, restart docky, and then end up with a dock in the right place, but if I do that I can't drag it to anywhere else at all.
I very much doubt it'd be an issue, but this was where my gnome do + docky theme was, until very recently (issue continues if gnome-do is not running).
When trying to drag the dock to the bottom of the right screen the debug output looks like:
[Info 02:05:08.598] Docky version: bzr docky r816
[Info 02:05:08.607] Kernel version: 2.6.31.14
[Info 02:05:08.608] CLR version: 2.0.50727.1433
[Debug 02:05:08.699] [SystemService] Using org.freedesktop.DeviceKit.Power for battery information
[Info 02:05:08.749] [DockServices] Dock services initialized.
[Info 02:05:08.876] [PluginManager] Loaded "Docky.Items,1.0".
[Info 02:05:08.884] Setting theme: Classic
[Info 02:05:09.151] [PluginManager] Loaded "Clock".
[Info 02:05:09.156] [PluginManager] Loaded "Network Manager".
[Info 02:05:09.219] [PluginManager] Loaded "CPU Monitor".
[Info 02:05:09.800] [DrawingService] Could not find 'thing.java [modified ] - editor', using fallback of 'application-default-icon'.
[Info 02:05:09.850] [DrawingService] Could not find 'thing.java [modified ] - editor', using fallback of 'application-default-icon'.
[Info 02:05:25.076] [DrawingService] Could not find 'clock', using fallback of 'application-default-icon'.
[...repeated...]
[Info 02:05:28.217] [DrawingService] Could not find 'thing.java [modified ] - editor', using fallback of 'application-default-icon'.
[...repeated...]
Which doesn't look too interesting to me at all, dunno?
I can't reproduce this as I don't have 2 monitors anymore. To the OP, do you still have this issue?