It's a long time since you posted this question but the problem is still around for many users so my reply can be usefull for some people. You should replace thermal pads with new thermal pads or with a thermal paste that is specially designed to replace thermal pads. Do not reuse old pads and do not replace pads with normal thermal paste like Arctic Silver. Both will lead to overheating and result to GPU or other BGA failure.
You can find apropriate thermal pads on Amazon or ebay. You should know how thik they are, how soft they are and how big they are before you order them.
Until now I have found only one thermal paste that can replace thermal pads. It is called K5-PRO and you can find videos of it on youtube
http://www.youtube.com/watch?v=e9v5MDivZfc
and it is avaliable on ebay
http://www.ebay.com/itm/261419411897