Sometimes I have a problem shutting down.
I get a box saying "a program is still running - GNOME settings daemon" and this just stays there.
I can workround the problem by cancelling the box and doing shutdown again but it would be nice to resolve the problem another way.
I don't know if this will help you, it hasn't helped me yet but here is another answer I found on this problem. It seems to me that it has something to do with graphics drivers as I am having the same issue of the proprietary driver not loading properly. I am trying to resolve it now, I will keep you updated.
http://ubuntuforums.org/showthread.php?t=2066978