Wow! That was easy when someone tells you! Ran Spybot, found a load of stuff... ran Trend, found nothing.... Deleted IE9 and installed Chrome! Gone! No more worries! Simplez!
Time to close the thread!

Was just asked how I did this so I will try and explain.

1. Humour and Aussiegeorge told me about 2 apps that might help. Spybot and Trend.
2. Ran the online Trend app but it found nothing.
3. Ran Spybot in Safemode and it found a ton of stuff that I didnt even understand. It removed them and then I booted normally.
4. Opened IE9 again and it did actually seem to run faster and pages opened quicker.
5. After clicking through a fewe sites... BANG, BOOM! There it was agin! Althoiugh, the pop-up window didnt actually show any ads. It just said that it couldnt connect to ad.yield.com (I just used that site because I cant remember the actually one it mentioned!)
6. That also proved that it wasnt only adtmt.com that was responsible for the pop-up because the sites did not match and as far as I could tell, they werent connected.
7. By now I was ready to put my foot through the computer until Humour suggested I try Chrome... which I then installed. Works like a charm... but now I had to get rid of IE9.
8. Searched for various ways of doing this but only found that it wasd possible to uninstall it through rolling back the IE9 update. This only reverted it back to IE8 and then found out that if I was to disable it all together certain sites wouldnt run so I just disabled the exe. file.
9. Went to this link and followed the destructions! Job done!
http://lifehacker.com/5164286/window...explorer-kinda