Not sure, but this could be a cookie issue. if the browser allows all cookies, including 3rd party cookies, then perhaps this is allowing the pop-ups.
In IE9 > Tools > Internet Options, then the Privacy tab, lower your settings slider for the Internet Zone to Medium, and test. If that fails, lower it again to Low, and test again.
Before testing, download a cookie cleaner utility like CCleaner from http://www.piriform.com/ccleaner and analyse then run the cleaner to remove all temp files, all temporary internet files, and all cookies. Beware, if there are some cookies you 'must' keep, head over to Options > Cookies and move the ons you want to the right hand column, before running the cleaner.
Do you get these pop-ups when you run your other browsers?
Recently upgaded to IE9 (on Windows7). Somewhere around that time (can't be sure it was exactly right away) I started getting some very annoying flashing popups that do not seem to be related to a particular website. They are advertisements from several mainstream companies, but there dosn't seem to be a "close" button or an "X". I have run Ad-Aware and Norton 360 as well as having the popup blocker turned on, but they are still there. Any hints how to get rid of them?