How do I stop explorer from opening pop ups while browsing with firefox as default.

I just bought a new hp laptop with windows 7. The first thing I did was install firefox 3.6.12 set as default, then thunderbird. When I visit a website I get pop ups that open in windows explorer.
I installed pop-up stopper free edition, but it didn't help.
I had firefox on my old PC running windows vista and pop-up stopper, and never had this problem.
I tried disabling IE by setting up a false proxy server, which I think helped, but then I couldn't use windows media center for internet tv, etc.
This is pretty frustrating, since my old setup really worked great.

I tried to remedy it by changing the default settings, but there are three settings that are ticked and that you can't disassociate with IE - two MHTML and one .url for internet shortcuts. Presuming the last is the reason the popups open in IE?

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