My sister had this problem a few days ago with popups that weren't related to IE. It took me 5 hours of constant scanning with Adaware And Spybot S&D plus scanning with a AVG 6.0 to get rid of the dam things.
I'm pretty sure you've checked for Viruses, we had some Trojans on that computer that might have had something to do with it. Either way it's fixed now.
Good Luck sorting it out
