Easiest way to most likely fix this is to download AdAware (possibly &/or similar apps) and run it.
It sounds to me not like a virus, but more like an Internet Explorer hitch that some sleezy pop-up vendor is taking advantage of. For example, I've seen pop-up widnows that shrink themselves or hide themselves or even place themself outside of the desktop's boundaries so you don't see them. Then that unseen window can periodically launch other pop-up windows all on it's own.
If this is the case you should be able to hit CTRL-ALT-DEL and look for any instances of IEXPLORER.EXE that are currently running. If you see'em, shut'em down.
I believe
AdAware (free) will seek out and remove this type of pest.
Someone correct me if I'm wrong. Since I use Mozilla this kind of stuff just doesn't happen.