this happens occasionally with my compiz + nvidia.
it might be triggered by opening/unminimizing windows while the other windows 
are "moved out" to show the desktop (but i haven't found a reliable way to 
reproduce this bug).
last time it happened, several of my windows became unreachable. after a short 
fight with keyboard shortcuts (alt+space move) and "expose" (which showed the 
windows but did not allow to activate it) the compiz finally crashed and the 
windows have returned to normal.

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Application dialogs becomes unreachable after show desktop
https://bugs.launchpad.net/bugs/370559
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