there is about two in the case one on the cpu, one on the video card, and one in the power supply. I do not know what the stock cooler, and i didnt not put too much thermal past.
Can you take a picture of the heatsink? Perhaps something bent or could be loose. I heard some Intel heatsinks lose their capacity to draw away heat when something plastic on it kind of melts or something.
Edit: Will try to find the thread that stated that, give me a moment.