Just because a browser is default doesn't mean it's opened all the time to see a site. Certain programs specifically search for different browsers. It's likely that you have a program that initiates when you excite a trigger and creates pop-ups. Using IE's poor pop up blocker you get spammed again and again with more and more pop-ups.
All that pop-up blockers do is disable code that's embedded into a page. The html code can be put in places where it can't be detected by the pop-up blocker, which is the problem for pop-ups that can't be stopped. But basically the pop-up blocker detects the code that looks something like:
<META HTTP-EQUIV="refresh" content"?; URL=?">
or
ONACTION="javascrip:window.open('?','?', 'HEIGHT=?, WIDTH=?)"
and ignores the action until the unblock button is pressed. Pop-ups are dangerous in that the source site is safe but the pop-up isn't. If it isn't protected, the pop-up can open another pop up and and that pop up another and etc. Such as when you have advertising enabled on this site and it shows you another site to see until you hit the "skip advertisement button". Sometimes those sites revert you another site, sometimes bad.
There are other ways of making pop ups happen, and other ways to use the internet explorer to hack into other peoples computers, which is why it's so scary. Such as with that facebook incident with FTV or those ads that pop up a message saying "are you sure you want to stray away from this offer" You may need a better anti-virus or malware detector...