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In order to be in sync, let's define unity views' numbers:
1 - 2
3 - 4
Normally, Ubuntu boots to view 1.
With keyboard shortcut I went to view 2. Opened here a gnome-terminal, and 
half-maximized it (with Ctrl-Alt-8 shortcut).
With keyboard shortcut I went back to view 1, back to view 2.
Now the terminal window was shifted to the left, so that it was covered by the 
Unity launcher.
Notes:
- Reproducable (at least if I reproduce it now)
- Doesn't seem to appear on view 1.
- Doesn't seem to appear if the terminal window size is set manually, rather 
than with Ctrl-Alt-8.
- Unity launcher is set to be always visible
Attached:
Screenshots before and after

ProblemType: Bug
DistroRelease: Ubuntu 11.10
Package: unity 4.28.0-0ubuntu2
ProcVersionSignature: Ubuntu 3.0.0-23.38-generic 3.0.36
Uname: Linux 3.0.0-23-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 1.23-0ubuntu4
Architecture: amd64
CompizPlugins: 
[core,bailer,detection,composite,opengl,compiztoolbox,decor,grid,mousepoll,regex,vpswitch,snap,gnomecompat,place,wall,move,resize,imgpng,animation,expo,session,workarounds,ezoom,staticswitcher,fade,scale,unityshell]
Date: Thu Jul 19 16:53:28 2012
InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111011)
SourcePackage: unity
UpgradeStatus: Upgraded to oneiric on 2012-03-26 (114 days ago)

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


** Tags: amd64 apport-bug oneiric running-unity
-- 
application window 'jumps' under the unity launcher
https://bugs.launchpad.net/bugs/1026623
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packagers, which is subscribed to compiz in Ubuntu.

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