ratbastid, I'm actually having the exact same problem. I've ran Hijack This, CWShredder, Ad-Aware, Spybot: Search and Destroy, and Symantec Anti-Virus. Most come up clean everytime, and those that show any problems fix them with ease. Even after this, every damn time I leave my PC for a while, I come back with 10 popups. Where the hell are they coming from? I'm pretty sure it's a new self-aware adware that's being made.
It keeps getting smarter and smarter. I'm about to format my freakin computer over a few damn popups that no program can eliminate.
I'd appreciate any other suggestions as well!
-Lasereth