Unity session stacks monitors on top of each other on startup

When using the Unity session with a dual monitor setup, the secondary display appear under the main display (at position 0,0 when it should be at 1920,0).
The monitor has to be moved using the NVidia settings panel but will happen again at next startup.

One thing to note is that when moved back to it's correct position, the secondary display has no wallpaper. It black at first but moving windows on that display will produce a nice "Windows 95" effect (the background doesn't redraw it self). Choosing a new wallpaper fixes this.

This behavior is exclusive to the Unity session, Gnome Shell behaves correctly.

ProblemType: Bug
DistroRelease: Ubuntu 16.10
Package: unity 7.5.0+16.10.20160906.1-0ubuntu1
ProcVersionSignature: Ubuntu 4.8.0-26.28-generic 4.8.0
Uname: Linux 4.8.0-26-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
.proc.driver.nvidia.gpus.0000.01.00.0: Error: [Errno 21] Is a directory: '/proc/driver/nvidia/gpus/0000:01:00.0'
.proc.driver.nvidia.registry: Binary: ""
.proc.driver.nvidia.version:
 NVRM version: NVIDIA UNIX x86_64 Kernel Module 367.57 Mon Oct 3 20:37:01 PDT 2016
 GCC version: gcc version 6.2.0 20161005 (Ubuntu 6.2.0-5ubuntu12)
.proc.driver.nvidia.warnings.fbdev:
 Your system is not currently configured to drive a VGA console
 on the primary VGA device. The NVIDIA Linux graphics driver
 requires the use of a text-mode VGA console. Use of other console
 drivers including, but not limited to, vesafb, may result in
 corruption and stability problems, and is not supported.
.tmp.unity_support_test.0:

ApportVersion: 2.20.3-0ubuntu8
Architecture: amd64
CompizPlugins: No value set for `/apps/compiz-1/general/screen0/options/active_plugins'
CompositorRunning: compiz
CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
CompositorUnredirectFSW: true
CurrentDesktop: Unity
Date: Thu Nov 3 11:00:14 2016
DistUpgraded: 2016-10-19 15:31:33,084 DEBUG icon theme changed, re-reading
DistroCodename: yakkety
DistroVariant: ubuntu
GraphicsCard:
 Subsystem: ASUSTeK Computer Inc. Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller [1043:8534]
 NVIDIA Corporation GM204 [GeForce GTX 970] [10de:13c2] (rev a1) (prog-if 00 [VGA controller])
   Subsystem: ASUSTeK Computer Inc. GM204 [GeForce GTX 970] [1043:8508]
InstallationDate: Installed on 2015-05-15 (538 days ago)
InstallationMedia: Ubuntu 15.04 "Vivid Vervet" - Beta amd64 (20150326)
LightdmLog: [+29062.52s] DEBUG: User /org/freedesktop/Accounts/User126 added
MachineType: ASUS All Series
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.8.0-26-generic root=UUID=ac70f6a6-c3ca-4a32-9847-163eb265642c ro quiet splash nouveau.blacklist=1 vt.handoff=7
SourcePackage: unity
UpgradeStatus: Upgraded to yakkety on 2016-10-19 (14 days ago)
dmi.bios.date: 04/24/2015
dmi.bios.vendor: American Megatrends Inc.
dmi.bios.version: 2401
dmi.board.asset.tag: To be filled by O.E.M.
dmi.board.name: Z97-A
dmi.board.vendor: ASUSTeK COMPUTER INC.
dmi.board.version: Rev 1.xx
dmi.chassis.asset.tag: To Be Filled By O.E.M.
dmi.chassis.type: 3
dmi.chassis.vendor: To Be Filled By O.E.M.
dmi.chassis.version: To Be Filled By O.E.M.
dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr2401:bd04/24/2015:svnASUS:pnAllSeries:pvrSystemVersion:rvnASUSTeKCOMPUTERINC.:rnZ97-A:rvrRev1.xx:cvnToBeFilledByO.E.M.:ct3:cvrToBeFilledByO.E.M.:
dmi.product.name: All Series
dmi.product.version: System Version
dmi.sys.vendor: ASUS
version.compiz: compiz 1:0.9.13.0+16.10.20160818.2-0ubuntu2
version.ia32-libs: ia32-libs N/A
version.libdrm2: libdrm2 2.4.70-1
version.libgl1-mesa-dri: libgl1-mesa-dri 12.0.3-1ubuntu2
version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
version.libgl1-mesa-glx: libgl1-mesa-glx 12.0.3-1ubuntu2
version.nvidia-graphics-drivers: nvidia-graphics-drivers-* N/A
version.xserver-xorg-core: xserver-xorg-core 2:1.18.4-1ubuntu6
version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.10.2-1ubuntu1
version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.7.1-1
version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.99.917+git20160706-1ubuntu1
version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.12-2
xserver.bootTime: Wed Nov 2 15:57:44 2016
xserver.configfile: /etc/X11/xorg.conf
xserver.errors:

xserver.logfile: /var/log/Xorg.0.log
xserver.outputs:

xserver.version: 2:1.18.4-1ubuntu6