So the problem seems to be at the system level, if it recurs in a new account.
USB and FireWire devices can sometimes affect startup, shutdown, wake, and sleep, so you should try disconnecting everything (including any hubs) except for keyboard/mouse and see if that has any effect.
Also, you can try doing a reset PRAM
http://support.apple.com/kb/HT1379
and if that does not help, reset SMC
http://support.apple.com/kb/HT3964
After the SMC reset, again try it with only keyboard/mouse connected. If the problem goes away, add your peripheral devices and check again.
If the problem continues, one thing you can try short of reinstalling the OS, is to apply the latest combo updater manually. That would be for 10.6.2 and you can download it here
http://www.apple.com/downloads/macosx/apple/macosx_updates/macosxv1062updatecomb o.html
Even if you already have 10.6.2, running the combo will reinstall all the changes at once, and this can sometimes resolve hard to diagnose issues.