On my home server running W2K3 and Exchange2003 I found that a reboot or shutdown takes extraordinary long (~20 min.). Maybe it is Ok that it takes so long and is so hard to bring down W2K3 :-)
I analysed the syslog and found that E2K3 seems to run into a timeout, I guess the order of shutting down processes is somehow wrong. Google told me that others have the same problem.
Thanx to the wonders of WMIC its rather simple to first terminate Exchange and then do the reboot or shutdown. Here is my reboot.cmd
Put a link on your desktop pointing to this file and you may reboot as usual by a mouse click. Shutdown is done similar, here is shutdown.cmd
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