I'm actually having a problem with python and compiz-fusion my self, and I can't run compiz-config. http://www.sabayonlinux.org/forum/viewtopic.php?f=53&t=10633
So I'm doing this from memory now. I also don't even know where the config file is.
When you open compiz-config, to the bottom-right, there is a thing that says backends & configuration, or something to that effect. When you click on it, it allows you to import and export the config file, and under that, it has a drop-box thing with three options. The first is for gnome, the second is flat-file (I don't know what that means either), and the the third is for kde. If yours is set to kde or gnome, turn it to flat-file and see if that helps. If it doesn't, then I have no idea what the problem is.
hope this helps
Somebody once said: "If you've got it you've got it, if you don't you don't." That statement was terribly flawed.