BleepingComputer.com: Computer won't run programs or shut down

I've been having trouble running certain programs and systems like defrag or virus scanners. They'll work for a little bit then start stalling, typically timing out or staying up indefinately. Also, when I log off, it says there are programs still running (there aren't) and if I force it to shut down anyway, it just stays at the logging off screen for ever. I tried setting my computer back and it helped a little, but I'd appreciate it if someone could tell me what's wrong.

I also finally managed to find a scanner that doesn't freeze up when I use it, and it says I don't have any spyware or anything so I'm really not sure what the problem is.