When I click "Shut Down" from the Start menu, Windows notifies me that it is logging off, then notifies me it is shutting down. That's good. My screen then goes black, but the computer itself never actually shuts off; it simply restarts. My BIOS settings have remained unchanged since I using Windows XP (different harddrive) and XP had no problems actually turning off the computer. I verified in the BIOS that all of the "wake on..." settings have been disabled. I went into Windows' Power Options control panel applet and made sure that the setting, "When shut down is clicked, perform the following action... Shut Down" I checked my keyboard and mouse device driver settings (they are PS2) to make sure there are no "wake on..." settings enabled there (and there aren't). I also checked my network adapter in device manager and did uncheck the "wake on..." feature there. I think I covered everything. I only installed a Print Driver (made for Vista x64), but the shut down issue was occuring before that anyway. My system specs are as follows...
Intel Core 2 Duo E6550
Crucial Ballistix 2Gb (2x1Gb)
EVGA 8800GTS 640Mb
Hitachi 80Gb HDD (Pata - was laying around so used it)
Plextor PX760A DVD-R/W
PC Power & Cooling Silencer 750