I noticed this bug in 12.04 with normal windows too:
1. Use ccsm to set a slow window open animation.
2. Right click on desktop and select Change Desktop Background.
3. You will see the bottom of the window is missing for a couple of frames 
during the open animation.

You have to be very observant, because the problem is only visible right
at the start of the animation. There's a gap above the bottom
border/shadow of the window.

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https://bugs.launchpad.net/bugs/932520

Title:
  Maximzed windows on start up don't show full window

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