So--Have you checked your preferences for pop-ups in Firefox?
Tools-->Options-->Content and there is a checkbox for "Block pop-up windows" or something similar. Be sure that it is checked.
If it is checked, click on the "Allowed Sites" button ext to it, and see if you have any entries in there. If not, then my next step would be to run Spybot, Ad-aware, etc to clean up your system.
Let me know if that works or not. I'm interested to see what happens.