Snoopy: You say you have pop-ups disabled, but check if someone didn't define exceptions.
It's under options->contents, you have the checkbox for "block pop-ups", and on the same line a button "exceptions", where you can define which sites are allowed pop-ups. I remember there was a malware that filled that "exceptions" part with loads of sites. So even if you get rid of the malware, the exceptions are still there.