(1) Do you have an spyware\adware blocker? If not a good free one is Spyware Blaster
BrightFort
You can either stay with the free version and do manual updates (monthly) or pay a donation fee and get automatic updates.
This blocks almost all spyware and adware programs that I run into on their way in (there are other programs that sweep them from your hardrive - like adaware - but my sweeps come up empty since using spyware blaster).
(2) Have you configured your browser to block popups? Firefox, IExp, and others allow you to configure your browser to block all popups automatically. Usually they display a message bar to say when this happens (sometimes you need those popup windows to login on some sites, and this allows you to tailor the popup blocker to allow them from that site - I had to allow popups to watch the tour de france from their official site).
In firefox it is under tools ... options ... content.
(3) One more place they can hide is in your registry file, but if you really reformatted this should be taken care of.
Enjoy.
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