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[TomasHnyk <tomashnyk@xxxxxxxxx>]

Adding a one second delay t ostartup application (in my case pidgin)
solved my issue, as per instructions here:
http://askubuntu.com/questions/28685/how-can-i-delay-a-specific-program-
on-startup

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https://bugs.launchpad.net/bugs/759898

Title:
  Title bar of applications which start before Unity does, gets hidden
  under panel

Status in Compiz:
  Triaged
Status in Unity:
  Triaged
Status in “compiz” package in Ubuntu:
  Triaged
Status in “unity” package in Ubuntu:
  Triaged

Bug description:
  Binary package hint: unity

  For dealing with an earlier bug I added a gnome terminal to my startup
  applications--Unity was not loading properly and this allowed me to do
  a clean shutdown.  Now Unity is working properly, but I still have the
  Gnome Terminal in my startup applications (select system settings and
  it is "Startup Applications" under the "Personal" category.

  When I log in, the terminal starts as expected, but it has its own
  menu bar (i.e. not integrated with the unity panel) and it is placed
  flush with the top of the screen (i.e. with the window's title bar
  behind the top panel).  Everything is fully functional, and I can use
  the ALT-click-drag combo to move it out of the way.  If I close the
  terminal and start a new one, the menu is integrated into the unity
  panel and it opens in the right place (just below, not behind, the top
  panel).

  Again, everything is fully functional, it just appears that the app
  from the startup applications is not properly integrated into unity.
  I assume all this info was transmitted, but I am on Natty 11.04 beta,
  and all packages are up to date as of the time of this filing.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.04
  Package: unity 3.8.6-0ubuntu1
  ProcVersionSignature: Ubuntu 2.6.38-8.42-generic 2.6.38.2
  Uname: Linux 2.6.38-8-generic x86_64
  NonfreeKernelModules: fglrx
  Architecture: amd64
  CompizPlugins: [core,bailer,detection,composite,opengl,decor,regex,animation,grid,imgpng,vpswitch,unitymtgrabhandles,move,compiztoolbox,gnomecompat,mousepoll,place,resize,workarounds,session,wall,wobbly,expo,ezoom,staticswitcher,fade,scale,unityshell]
  CompositorRunning: compiz
  Date: Wed Apr 13 09:55:46 2011
  DistUpgraded: Log time: 2011-03-31 22:23:06.607321
  DistroCodename: natty
  DistroVariant: ubuntu
  DkmsStatus:
   psmouse, 2.6.35-22-generic, 2.6.35-24-generic, x86_64: built 
   fglrx, 8.840, 2.6.38-8-generic, x86_64: installed 
   fglrx, 8.840, 2.6.38-7-generic, x86_64: installed 
   virtualbox-ose, 4.0.4, 2.6.38-8-generic, x86_64: installed 
   virtualbox-ose, 4.0.4, 2.6.38-7-generic, x86_64: installed
  EcryptfsInUse: Yes
  ExecutablePath: /usr/bin/compiz-decorator
  GraphicsCard:
   ATI Technologies Inc Redwood [Radeon HD 5600 Series] [1002:68c1] (prog-if 00 [VGA controller])
     Subsystem: Hewlett-Packard Company Device [103c:1449]
  InstallationMedia: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
  InstallationMedia_: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
  InstallationMedia__: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
  InstallationMedia___: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
  InterpreterPath: /bin/dash
  JockeyStatus: xorg:fglrx - ATI/AMD proprietary FGLRX graphics driver (Proprietary, Enabled, In use)
  MachineType: Hewlett-Packard HP Pavilion dv7 Notebook PC
  ProcEnviron:
   LANGUAGE=en_US:en
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-2.6.38-8-generic root=UUID=59ba328b-3b67-4815-81de-8488735fba83 ro quiet splash vt.handoff=7
  ProcVersionSignature_: Ubuntu 2.6.38-8.42-generic 2.6.38.2
  ProcVersionSignature__: Ubuntu 2.6.38-8.42-generic 2.6.38.2
  ProcVersionSignature___: Ubuntu 2.6.38-8.42-generic 2.6.38.2
  Renderer: Unknown
  SourcePackage: unity
  UpgradeStatus: Upgraded to natty on 2011-04-11 (2 days ago)
  dmi.bios.date: 05/17/2010
  dmi.bios.vendor: Hewlett-Packard
  dmi.bios.version: F.07
  dmi.board.asset.tag: Base Board Asset Tag
  dmi.board.name: 1449
  dmi.board.vendor: Hewlett-Packard
  dmi.board.version: 65.19
  dmi.chassis.type: 10
  dmi.chassis.vendor: Hewlett-Packard
  dmi.chassis.version: N/A
  dmi.modalias: dmi:bvnHewlett-Packard:bvrF.07:bd05/17/2010:svnHewlett-Packard:pnHPPaviliondv7NotebookPC:pvr048D100000242B20000020000:rvnHewlett-Packard:rn1449:rvr65.19:cvnHewlett-Packard:ct10:cvrN/A:
  dmi.product.name: HP Pavilion dv7 Notebook PC
  dmi.product.version: 048D100000242B20000020000
  dmi.sys.vendor: Hewlett-Packard
  version.compiz: compiz 1:0.9.4+bzr20110411-0ubuntu1
  version.fglrx-installer: fglrx-installer N/A
  version.ia32-libs: ia32-libs 20090808ubuntu12
  version.libdrm2: libdrm2 2.4.23-1ubuntu6
  version.libgl1-mesa-dri: libgl1-mesa-dri 7.10.2-0ubuntu1
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 7.10.2-0ubuntu1
  version.xserver-xorg: xserver-xorg 1:7.6+4ubuntu3
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:6.14.0-0ubuntu4
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.14.0-4ubuntu7
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:0.0.16+git20110107+b795ca6e-0ubuntu7

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