I get this effect quite often with firefox. If I right click on a link
sometimes (I haven't actually worked out when), the menu comes up in
behind the application and you can't use it. In this case, I can get
around it by minimising and restoring the firefox window, I don't need
to restart compiz. I am using the AMD fglrx driver with an HD 3400.

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

Title:
  menu application appears behind window application

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