Found a Microsoft article that explains what is going on. Check out 555025. The solution is what SteveB7 suggested. Notice the disclaimer for this solution though. Gotta love Microsoft.
I have the same problem although the average shutdown time is about 15 minutes for me. I found the microsoft article q322837 about having these problems after you install SP2 or 3 for exchange 2000. They say that it is safe to ignore so I am wondering whether this is an issue that they have...
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