Comment 9 for bug 563161

I had this same problem. I checked into it and it turned out it was because I had been running emerald before I upgraded and the old emerald config's were lying around in my home folder, but I didn't reinstall emerald. So it tried to start it each time it booted.

I removed it from my startup programs list and added this: "compiz --replace" in its place.

This'll work if you're only using gnome. If you have KDE (or other), you'll need to have it check to see if you're running gnome or KDE and start compiz only if you're using gnome.

I wrote a simple script to do this (attached).