It appears the problem might be that the Unity plugin is being tricked
into creating additional panels when they're not needed. And possibly
getting the stacking order wrong too.

There are two pieces of evidence for this:
  1. The panel shadow gets darker when it's corrupt, suggesting multiple panels 
are present.
  2. This command starts showing multiple results instead of just one when the 
corruption occurs:
         xwininfo -children -root | grep panel

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https://bugs.launchpad.net/bugs/769957

Title:
  Unity panel turns black and/or corrupt when toggling Compiz plugins

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