This is really annoying. Happens on both of my fully-updated 12.04 LTS
workstations every-other week or so.

I tried compiz --replace but it isn't reliable. Sometimes leaves me with no 
window boarders and no way to recover the desktop. Best solution I found was to 
kill the desktop with:
Alt + PrintScr + K 
Not elegant, but works. 

$ uname -a
Linux hostname-l 3.2.0-030200rc5-generic #201112091935 SMP Sat Dec 10 00:36:07 
UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

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https://bugs.launchpad.net/bugs/735162

Title:
  menu application appears behind window application

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https://bugs.launchpad.net/compiz/+bug/735162/+subscriptions

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