It's also possible for compiz to lose two separate application window at
once (so that they behave like they are 'always on top'). I currently
have both Thunderbird and gnome-terminal behaving like this.

When a window gets in this state and you minimize it, compiz doesn't
draw it any more but unity-launcher still indicates it is the window
with foucs (via the arrow to the right of the application icon).

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https://bugs.launchpad.net/bugs/758253

Title:
  unity-compiz develops focus problems and sends input to minimized
  windows

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