Looks like a regular virus type deal. No viruses show up in scans from free-av, clamwin, spyware has been removed with ad-aware, microsoft beta, spybot
There was something called wuamk032.exe which i removed and restored all the registry settings
For some reason the task manager, regedit, cmd, and some various other things like that don't work
Everything is accessible in safe mode.
Anybody have any ideas?
Thanks.

Sounds like your sytem is still infected by some nasties.

Go HERE and follow the instructions carefully.

Once you have done that, go HERE for instructions on how to post your Hijackthis log.

Regards Howard

You probably have some process running in the background and blocking access to cmd, etc. try doing what hopkinso said and check out start up