first things first, and you said it yourself - do a clean install! MS recommend it highly and it is worth the pain.
there may be a way to fix your problem but i wouldnt spend anytime fixing things on an upgraded version when a clean install will give much better results in the long run. What if you hit more problems futher down the road? You'll always be thinking "was it because i didnt do a clean install?!"
do that first and if it still doesnt work feel free to come back to this post and flame me for making you waste four hours!