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?
I could find the IE7 entry in the add/remove programs so used this method instead
Copy all the .dll and .exe to
Then goto C:\windows\$NtUninstallie7bet2p$\spuninst\
Right click on spuninst.inf and goto Install
Rename spuninst.txt to spuninst.bat
However, now I have trouble with IE6 because most links that pop open a window create an extra blank window. Also some links create many (about 15) blank windows.
Probably the method above was not able to replace the files.
IE6 wont install on itself and repair the IE6 install.