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I had this problem to. It took me forever to figure it out, but you have to add compiz-manager to your startup options. You can do this by going to SYSTEM-->Preferences-->Personal-->Sessions. Click on add, name it whatever and the command should be compiz-manager. After a reboot CCSM settings take place.
On another related note. I had a hard time getting emerald themes to work. Created a shortcut that auto ran "emerald --replace". Now my themes work.
Good Luck
Chris
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