I always manage to bugger up my settings so that CompizFusion won’t start correctly on log-in, and drops back to MetaCity. I think it’s to do with the gconf settings, and although I could nuke the ~/.gconf folder, I’m not sure if this entirely works (will try again just prior to 9.10 install at end of month!).
Anyway, I fix it by putting a script with a delay into my Startup Applications setup to start Compiz and use the Emerald window manager as follows:
compiz --replace &
Fixes things 99% of the time to boot cleanly into Compiz, though about 1% of the time it doesn’t. Who knows what the hell’s going on…