Public bug reported:

Every time I reboot or log out and back in again, The layout of the displays is 
incorrect.
Correcting the layout is a bit 'hit and miss' as the changed layout is not 
always applied correctly.

There was a massive improvement after upgrading to 16.04 from 14.04.
Previously, the upper display did not render pixels consistently. The
upgrade corrected this.

The upper display (29") is connected to the NVIDIA Corporation GK107
[GeForce GT 740] display card and the lower display (23") is connected
to the on-board Intel Integrated Graphics Controller.

I hope this information is useful. Thanks for your efforts...

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: xorg 1:7.7+13ubuntu3
ProcVersionSignature: Ubuntu 4.4.0-62.83-generic 4.4.40
Uname: Linux 4.4.0-62-generic x86_64
.tmp.unity_support_test.0:
 
ApportVersion: 2.20.1-0ubuntu2.5
Architecture: amd64
CompizPlugins: 
[core,composite,opengl,decor,move,regex,resize,mousepoll,animation,wall,place,compiztoolbox,grid,gnomecompat,fade,workarounds,vpswitch,snap,imgpng,scale,session,expo,ezoom,switcher]
CompositorRunning: None
CurrentDesktop: GNOME-Flashback:Unity
Date: Fri Feb 17 21:59:43 2017
DistUpgraded: Fresh install
DistroCodename: xenial
DistroVariant: ubuntu
ExtraDebuggingInterest: Yes, if not too technical
GraphicsCard:
 Intel Corporation 2nd Generation Core Processor Family Integrated Graphics 
Controller [8086:0122] (rev 09) (prog-if 00 [VGA controller])
   Subsystem: Gigabyte Technology Co., Ltd 2nd Generation Core Processor Family 
Integrated Graphics Controller [1458:d000]
 NVIDIA Corporation GK107 [GeForce GT 740] [10de:0fc8] (rev a1) (prog-if 00 
[VGA controller])
   Subsystem: Palit Microsystems Inc. GK107 [GeForce GT 740] [1569:0fc8]
InstallationDate: Installed on 2014-05-28 (995 days ago)
InstallationMedia: Ubuntu 14.04 LTS "Trusty Tahr" - Release amd64 (20140417)
MachineType: Gigabyte Technology Co., Ltd. Z68XP-UD3P
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-62-generic 
root=UUID=71be335b-0f03-461d-b458-0b40a18be8ab ro quiet splash 
crashkernel=384M-:128M crashkernel=384M-:128M crashkernel=384M-:128M 
crashkernel=384M-:128M crashkernel=384M-:128M crashkernel=384M-:128M 
crashkernel=384M-:128M crashkernel=384M-:128M crashkernel=384M-:128M 
crashkernel=384M-:128M crashkernel=384M-:128M crashkernel=384M-:128M 
crashkernel=384M-:128M crashkernel=384M-:128M crashkernel=384M-:128M 
vt.handoff=7
SourcePackage: xorg
Symptom: display
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 09/01/2011
dmi.bios.vendor: Award Software International, Inc.
dmi.bios.version: F5
dmi.board.name: Z68XP-UD3P
dmi.board.vendor: Gigabyte Technology Co., Ltd.
dmi.board.version: x.x
dmi.chassis.type: 3
dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
dmi.modalias: 
dmi:bvnAwardSoftwareInternational,Inc.:bvrF5:bd09/01/2011:svnGigabyteTechnologyCo.,Ltd.:pnZ68XP-UD3P:pvr:rvnGigabyteTechnologyCo.,Ltd.:rnZ68XP-UD3P:rvrx.x:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvr:
dmi.product.name: Z68XP-UD3P
dmi.sys.vendor: Gigabyte Technology Co., Ltd.
version.compiz: compiz 1:0.9.12.2+16.04.20160823-0ubuntu1
version.ia32-libs: ia32-libs N/A
version.libdrm2: libdrm2 2.4.70-1~ubuntu16.04.1
version.libgl1-mesa-dri: libgl1-mesa-dri 12.0.6-0ubuntu0.16.04.1
version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
version.libgl1-mesa-glx: libgl1-mesa-glx 12.0.6-0ubuntu0.16.04.1
version.xserver-xorg-core: xserver-xorg-core 2:1.18.4-0ubuntu0.2
version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.10.1-1ubuntu2
version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.7.0-1
version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.99.917+git20160325-1ubuntu1.2
version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.12-1build2
xserver.bootTime: Fri Feb 17 21:25:03 2017
xserver.configfile: default
xserver.devices:
 input        Power Button         KEYBOARD, id 6
 input        Power Button         KEYBOARD, id 7
 input        Telink Wireless Receiver KEYBOARD, id 8
 input        Telink Wireless Receiver KEYBOARD, id 9
 input        AT Translated Set 2 keyboard KEYBOARD, id 10
xserver.errors:
 Failed to load module "nvidia" (module does not exist, 0)
 Failed to load module "nvidia" (module does not exist, 0)
 NOUVEAU(G0): [XvMC] Failed to initialize extension.
xserver.logfile: /var/log/Xorg.0.log
xserver.version: 2:1.18.4-0ubuntu0.2

** Affects: xorg (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug ubuntu xenial

** Attachment added: "Screenshots showing correct and wrong layouts"
   
https://bugs.launchpad.net/bugs/1665796/+attachment/4821076/+files/Screenshots.png

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https://bugs.launchpad.net/bugs/1665796

Title:
  multi-display layout corrupt after reboot or log out/in

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