Would it be the network?
I too have this problem. My "old" machine is networked to the "New" machine. If I try to shut it down it does as above. However if I shut down the new machine, the old one works perfectly!! So in my case it seems to be the network link.
I'll try the MSCONFIG tip but I can't prove it as I think I fried my network card during efforts to remove bugbear. However it is shutting down perfectly without the network at present.