I'm currently in the same boat. I'm working on what was once a massively infected machine. I took the hard drive out, scanned it w/ Symantec Corp. Ed., McAfee command-line scanner, Trend scanner, and AVG. Then I reinstalled the hard drive in the machine, and installed AVAST. BTW, every single one of those virus products found some sort of virus.
Anyway... Initially, I couldn't run SpyBot or SuperAntiSpyware. I would click on them, but it looked like nothing would happen. I pulled up task manager and noticed that if I tried opening them repeatedly, you could see them appear in the task list, then vanish.
Finally, after more scanning with AVAST (and I loaded temporarily on the machine AVG), I was able to get SpyBot working. But I still can't get SuperAntiSpyware to kick off.
This machine has been in my possession for a couple of weeks, so it wasn't hit by the latest UPS virus. But I sure would feel better if I could get SuperAntiSpyware to run.