A few suggestions
What was the last thing you installed on this system?
Some AV software scan the HDD on shut down, Try disabling any AV software on this system and try shutting down.
Apply latest service pack.
Run manufacturers diags on the machine to eliminate a hardware problem although I think this unlikely.
Shaun: I have had the problem before, with little or no success at discovering the problem in my system. However, I did find a freeware utility "ShutDownPro" that usually overcomes the problem.
Here is a link in Download.com to download ant try it for yourself:
After it restarts, press F8, and at the menu select Safe mode and then see if when you shutdown if that makes a difference. You might also try the step-by-step confirmation, see if there are any problems during the bootup that may not be noticeable during a regular startup.
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