This should be fixed now.

** Changed in: compiz (Ubuntu)
       Status: Triaged => Fix Released

** Changed in: compiz
       Status: Triaged => Fix Committed

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https://bugs.launchpad.net/bugs/785663

Title:
  compiz does not retain window positioning after restart

Status in Compiz:
  Fix Committed
Status in Compiz Core:
  Confirmed
Status in “compiz” package in Ubuntu:
  Fix Released

Bug description:
  Binary package hint: compiz

  After compiz restart (eg. when compiz --replace or by killing blocked
  compiz process), windows are incorrectly placed - most often shifted
  down by height of the title bar, but gnome-terminal windows are placed
  to the top left corner. Assignment of windows to virtual desktops is
  not preserved as well.  There are also problems with cairo-dock's
  windows; after compiz restarts, the dock is stacked below other
  windows instead of above. I have to restart cairo-dock, but then the
  desklets are not anymore mapped to the widget layer and it is
  necessary to re-enter the window matching condition (type=Utility
  &class=Cairo-dock) in the widget plugin configuration to restore the
  order.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.04
  Package: compiz 1:0.9.4+bzr20110415-0ubuntu2
  ProcVersionSignature: Ubuntu 2.6.39-1.6-generic 2.6.39-rc6
  Uname: Linux 2.6.39-1-generic x86_64
  Architecture: amd64
  CompizPlugins: 
[core,bailer,detection,composite,opengl,decor,compiztoolbox,widget,resize,annotate,copytex,mousepoll,dbus,text,imgjpeg,obs,imgpng,extrawm,regex,grid,thumbnail,gnomecompat,resizeinfo,imgsvg,place,move,group,shift,animation,ring,wobbly,session,animationaddon,workarounds,cube,scale,expo,rotate]
  CompositorRunning: compiz
  DRM.card0.DVI.D.1:
   status: connected
   enabled: enabled
   dpms: On
   modes: 1920x1200 1600x1200 1280x1024 1280x1024 1280x960 1152x864 1024x768 
1024x768 1024x768 832x624 800x600 800x600 800x600 800x600 640x480 640x480 
640x480 640x480 720x400
   edid-base64: 
AP///////wBMLbYCNDJVSC0RAQOANCCgKlrRp1ZLmyQTUFS/74CpQIGAgUBxTwEBAQEBAQEBKDyAoHCwI0AwIDYABkQhAAAaAAAA/QA4Sx5REQAKICAgICAgAAAA/ABTeW5jTWFzdGVyCiAgAAAA/wBIUzFQQjAwMjgyCiAgAJo=
  DRM.card0.LVDS.1:
   status: connected
   enabled: enabled
   dpms: On
   modes: 1680x1050 1400x1050 1280x1024 1440x900 1280x960 1280x854 1280x800 
1280x720 1152x768 1024x768 800x600 848x480 720x480 640x480
   edid-base64:
  DRM.card0.VGA.1:
   status: disconnected
   enabled: disabled
   dpms: Off
   modes: 
   edid-base64:
  Date: Fri May 20 11:11:51 2011
  DistUpgraded: Log time: 2011-05-02 09:12:36.019370
  DistroCodename: natty
  DistroVariant: ubuntu
  GraphicsCard:
   ATI Technologies Inc Mobility Radeon HD 3400 Series [1002:95c4] (prog-if 00 
[VGA controller])
     Subsystem: Acer Incorporated [ALI] Device [1025:0138]
  InstallationMedia: Ubuntu 9.10 "Karmic Koala" - Release amd64 (20091027)
  InstallationMedia_: Ubuntu 9.10 "Karmic Koala" - Release amd64 (20091027)
  MachineType: Acer TravelMate 6593
  PackageArchitecture: all
  PccardctlIdent:
   Socket 0:
     no product info available
   Socket 1:
     product info: "O2Micro", "SmartCardBus Reader", "V1.0", ""
     manfid: 0xffff, 0x0001
  PccardctlStatus:
   Socket 0:
     no card
   Socket 1:
     5.0V 16-bit PC Card
     Subdevice 0 (function 0) [unbound]
  ProcEnviron:
   LANGUAGE=en_US:en
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-2.6.39-1-generic 
root=UUID=42face5e-6d34-4155-ad18-d701af6a3ec6 ro splash vt.handoff=7
  ProcVersionSignature_: Ubuntu 2.6.39-1.6-generic 2.6.39-rc6
  Renderer: Unknown
  SourcePackage: compiz
  UpgradeStatus: Upgraded to natty on 2011-05-02 (17 days ago)
  dmi.bios.date: 12/23/2008
  dmi.bios.vendor: Phoenix Technologies LTD
  dmi.bios.version: V1.11
  dmi.board.name: FourPeaks
  dmi.board.vendor: Acer
  dmi.board.version: Rev
  dmi.chassis.type: 10
  dmi.chassis.vendor: Acer
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnPhoenixTechnologiesLTD:bvrV1.11:bd12/23/2008:svnAcer:pnTravelMate6593:pvr0100:rvnAcer:rnFourPeaks:rvrRev:cvnAcer:ct10:cvrN/A:
  dmi.product.name: TravelMate 6593
  dmi.product.version: 0100
  dmi.sys.vendor: Acer
  version.compiz: compiz 1:0.9.4+bzr20110415-0ubuntu2
  version.ia32-libs: ia32-libs 20090808ubuntu13
  version.libdrm2: libdrm2 2.4.25+git20110415.ba11501b-0ubuntu0sarvatt
  version.libgl1-mesa-dri: libgl1-mesa-dri 
7.11.0+git20110502.9cb800a9-0ubuntu0sarvatt
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 
7.11.0+git20110502.9cb800a9-0ubuntu0sarvatt
  version.xserver-xorg: xserver-xorg 1:7.6+4ubuntu3
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99+git20110502.8f8bbf62-0ubuntu0sarvatt
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.15.0+git20110420.0944e2d5-0ubuntu0sarvatt
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:0.0.16+git20110323.8378443b-0ubuntu0sarvatt
  --- 
  .tmp.unity.support.test.0:
   
  ApportVersion: 1.93-0ubuntu2
  Architecture: i386
  CompizPlugins: 
[core,bailer,detection,composite,opengl,imgjpeg,copytex,decor,move,compiztoolbox,resize,text,extrawm,mousepoll,vpswitch,dbus,thumbnail,imgsvg,wobbly,shift,cube,regex,widget,annotate,ring,imgpng,place,gnomecompat,resizeinfo,rotate,unitymtgrabhandles,animation,expo,scale,animationaddon,session,workarounds,scaleaddon]
  CompositorRunning: compiz
  DistUpgraded: Log time: 2012-01-24 17:34:52.134545
  DistroCodename: precise
  DistroRelease: Ubuntu 12.04
  DistroVariant: ubuntu
  GlAlternative: lrwxrwxrwx 1 root root 24 May  3  2010 
/etc/alternatives/gl_conf -> /usr/lib/mesa/ld.so.conf
  GraphicsCard:
   Advanced Micro Devices [AMD] nee ATI Radeon Mobility X700 (PCIE) [1002:5653] 
(prog-if 00 [VGA controller])
     Subsystem: Acer Incorporated [ALI] Device [1025:0070]
  MachineType: Acer, inc. TravelMate 8100
  Package: compiz 1:0.9.7.0~bzr2995-0ubuntu5
  PackageArchitecture: all
  PccardctlIdent:
   Socket 0:
     no product info available
  PccardctlStatus:
   Socket 0:
     no card
  ProcEnviron:
   TERM=xterm
   PATH=(custom, user)
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/ubuntu/boot/vmlinuz-3.2.0-16-generic-pae 
root=/dev/sda6 ro quiet
  ProcVersionSignature: Ubuntu 3.2.0-16.25-generic-pae 3.2.6
  Tags:  precise precise ubuntu compiz-0.9
  Uname: Linux 3.2.0-16-generic-pae i686
  UnreportableReason: This is not an official Ubuntu package. Please remove any 
third party package and try again.
  UpgradeStatus: Upgraded to precise on 2012-01-27 (34 days ago)
  UserGroups: adm admin audio cdrom dialout dip lpadmin netdev plugdev scanner 
video
  dmi.bios.date: 04/26/05
  dmi.bios.vendor: Acer
  dmi.bios.version: 3C23
  dmi.board.name: Kingfisher
  dmi.board.vendor: Acer, Inc.
  dmi.board.version: Not Applicable
  dmi.chassis.type: 1
  dmi.chassis.vendor: Acer, Inc.
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnAcer:bvr3C23:bd04/26/05:svnAcer,inc.:pnTravelMate8100:pvrNotApplicable:rvnAcer,Inc.:rnKingfisher:rvrNotApplicable:cvnAcer,Inc.:ct1:cvrN/A:
  dmi.product.name: TravelMate 8100
  dmi.product.version: Not Applicable
  dmi.sys.vendor: Acer, inc.
  version.compiz: compiz 1:0.9.7.0~bzr2995-0ubuntu5
  version.libdrm2: libdrm2 2.4.31+git20120214.9b3ad51a-0ubuntu0sarvatt
  version.libgl1-mesa-dri: libgl1-mesa-dri 
8.0.1+git20120223+8.0.d38a2952-0ubuntu0sarvatt
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 
8.0.1+git20120223+8.0.d38a2952-0ubuntu0sarvatt
  version.xserver-xorg-core: xserver-xorg-core 
2:1.11.99.903+git20120224.38000e7d-0ubuntu0sarvatt
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 
1:2.6.99.901+git20120126-0ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99+git20120223.688c8a54-0ubuntu0sarvatt
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.17.0+git20120223.a647aff5-0ubuntu0sarvatt
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau N/A

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