I've never had a problem with Pop-Up-Killer. Somehow it knew which windows I wanted to pop up and which one I wanted it to kill.
Originally posted by hostensteffa
Your best bet in my opinion is to just manually close the windows, it normally shouldn't be a big deal unless you're surfing a bunch of porn sites or something. Most pop up stoppers will close not just popups but any new window that is open, so for instance we'll use these boards as an example, how normally you could click on a link that some of the posters provide and it would pop up new, it would stop that as well. That is unless you pay for one.