First, what happens when you follow these instructions to repair IE6? (I'm assuming it's giving you an error about installing an older version over a newer version, but I'd like to verify that.)

What I'd do is reinstall IE7 Beta 2, then attempt a proper uninstallation, following the instructions available by clicking here. It may not work, but it should do the trick.

Hope this helps,

P.S. Are you sure the extra windows are not just popups from those sites with the actual advert being removed?