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
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