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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.

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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

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Welcome to Ask Ubuntu! Whilst this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference. –  Eliah Kagan Dec 23 '12 at 11:07

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