Ok we need to know:
Is the thermal paste the right amount? (Pea dot size)
And wiggle around the cooler a little when the computer is off to see if its on firmly. It its loose and moving around you will most likely have to check those pins. Make sure that the cooler pins all click in. You will hear the click, its ok if the mobo bends a little. If it doesnt click then take the pins out check if they arent bent and put them back in. Also, this is a major how much paste is on the cooler.