Also, I created a new user account to test this issue. This problem is
not exhibited with the new user account, although both that account and
my existing account where the problem exists have the same settings in
monitors.xml.

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https://bugs.launchpad.net/bugs/1133046

Title:
  Second monitor's desktop is placed on top of the first at login

Status in “xorg” package in Ubuntu:
  New

Bug description:
  I have my laptop hooked up to an external monitor. Each time I log in,
  both monitors occupy the same space. I have to open the Displays
  section of System Settings and drag the monitors around to re-postion
  them.

  I have attached a screenshot to illustrate. It can be seen in the
  Displays dialog that the salmon-colored Laptop screen is behind the
  external monitor (its edges are barely visible).

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: xorg 1:7.7+1ubuntu4
  ProcVersionSignature: Ubuntu 3.5.0-25.38-generic 3.5.7.4
  Uname: Linux 3.5.0-25-generic x86_64
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.6.1-0ubuntu10
  Architecture: amd64
  CompizPlugins: 
[core,composite,opengl,compiztoolbox,decor,vpswitch,snap,mousepoll,resize,place,move,wall,grid,regex,imgpng,session,gnomecompat,animation,fade,unitymtgrabhandles,workarounds,scale,expo,ezoom,unityshell]
  CompositorRunning: compiz
  Date: Mon Feb 25 18:03:00 2013
  DistUpgraded: 2012-10-23 23:56:55,912 DEBUG enabling apt cron job
  DistroCodename: quantal
  DistroVariant: ubuntu
  ExtraDebuggingInterest: Yes
  GraphicsCard:
   Intel Corporation Mobile GM965/GL960 Integrated Graphics Controller 
(primary) [8086:2a02] (rev 03) (prog-if 00 [VGA controller])
     Subsystem: Toshiba America Info Systems Device [1179:ff1c]
     Subsystem: Toshiba America Info Systems Device [1179:ff1c]
  InstallationDate: Installed on 2012-09-22 (156 days ago)
  InstallationMedia: Ubuntu 12.04.1 LTS "Precise Pangolin" - Release amd64 
(20120823.1)
  MachineType: TOSHIBA Satellite A305
  MarkForUpload: True
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.5.0-25-generic 
root=UUID=dcedb5c2-7281-4ce4-9463-6fdf34bc89c5 ro quiet splash vt.handoff=7
  SourcePackage: xorg
  Symptom: display
  UpgradeStatus: Upgraded to quantal on 2012-10-24 (124 days ago)
  dmi.bios.date: 02/13/2009
  dmi.bios.vendor: INSYDE
  dmi.bios.version: 1.80
  dmi.board.asset.tag: Base Board Asset Tag
  dmi.board.name: Base Board Product Name
  dmi.board.vendor: Intel Corp.
  dmi.board.version: Base Board Version
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 1
  dmi.chassis.vendor: Chassis Manufacturer
  dmi.chassis.version: Chassis Version
  dmi.modalias: 
dmi:bvnINSYDE:bvr1.80:bd02/13/2009:svnTOSHIBA:pnSatelliteA305:pvrPSAG0U-02701V:rvnIntelCorp.:rnBaseBoardProductName:rvrBaseBoardVersion:cvnChassisManufacturer:ct1:cvrChassisVersion:
  dmi.product.name: Satellite A305
  dmi.product.version: PSAG0U-02701V
  dmi.sys.vendor: TOSHIBA
  version.compiz: compiz 1:0.9.8.6-0ubuntu1
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.39-0ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 9.0-0ubuntu1
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 9.0-0ubuntu1
  version.xserver-xorg-core: xserver-xorg-core 2:1.13.0-0ubuntu6.1
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.3-0ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.99.99~git20120913.8637f772-0ubuntu1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.20.9-0ubuntu2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.2-0ubuntu3

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