Same thing here on 12.04 (old, I know)

Linux 3.13.0-39-generic #66~precise1-Ubuntu SMP Wed Oct 29 09:56:49 UTC
2014 x86_64 x86_64 x86_64 GNU/Linux

Unity 5.20.0
Compiz 0.9.7.12


Let me know if you guys need any more data! I've just confirmed that the 
previous 'compix --replace' works, though it's a pain. It screws up all of my 
workspace layouts. 


Thanks!

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

Title:
  menu application appears behind window application

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