Having seen this become obviously a big problem.  I have decided to do a podcast on this and talk about the solutions on it.
[display_podcast]
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Show Notes for Shutting Down Vista:

• shutdown /s /f /t 00
• VISTA ShutDown Problem
• Windows Key>Right X 3>Enter
• Changing Hibernation into Shutdown mode
• HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control (right click on WaitToKillServiceTimeout and pick something like 1000 or lower in Milliseconds)
• Nvidia 100.65 Driver Problems