It sounds like you didn't seat the stock cooler properly. I think the stock cooler comes with the thermal paste pre-applied, so it might not be usable if you re-seat the heatsink. In that case you'll have to buy some thermal paste. If you do buy some new thermal paste, make sure you wipe off the old thermal paste from both the heatsink and the cpu (its often recommended to use a 90% alcohol solution, but 70% isopropyl from your local drug store works just fine).