I don't know how to fix the problem, but you can disable the effects that don't work correctly. Install the configuration tool for compiz (if you haven't already)
Code:
sudo apt-get install compizconfig-settings-manager
then you can access it from System->Preferences->Advanced Desktop Effects Settings. From here you can disable what doesn't work. A number of other users have been claiming problems with 9600 cards, so it seems to be a generalized problem, not specific to your computer or the fact that it is an apple.
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