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.
(hide) If you don't want other users to know what you are doing you can change into cloak mode in Settings (paying members only). (pauloaguia) (show all tips)