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)
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.
sudo apt-get install compizconfig-settings-manager