I am certain that W2K can be shut down the same way as XP, by just going through the Start>Turn off Computer process. I just cannot remember how to get the option .
Have you trid removing those entries in safe mode at all? If not, please do so.

Go here and download then run Silent Runners.vbs. It generates a log. Please post the information back in this thread.
If you have a script blocking program, please allow the file to run. It is not malicious.