When you change with xrandr the screen resolution and proprieties, compiz needs to be restarted in order to get the correct area. TO REPRODUCE: For example try to use 800x600, run compiz, then change display size to 1024x768 (from a smaller to a bigger resolution), or try to rotate your screen using xrandr, you will get a black area.
https://bugs.freedesktop.org/show_bug.cgi?id=11439
*** This bug has been marked as a duplicate of bug 11439 ***
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