It has to be the HSF installation, especially if its the stock one. Or if your using a 3rd party with the 4 push pin style.
One or perhaps 2 of those 4 pins are not on securely.
If you want to try to reinstall, try these steps:
1.) Turn the black knobs toward the arrows on them, pull up to uninstall the HSF.
2.) When the HSF is off, clean off all thermal grease from the CPU and the bottom of the HSF. Rubbing alcohol (90%) is recommended, with lint free cloth.
3.) Turn all 4 black knobs the opposite of the arrow.
4.) Reapply the thermal grease according to its instructions.
5.) When setting the HSF on, be sure the black pins are up, and the handles are turned opposite of the arrows. Place it on, making sure the white clamps pass through the holes.
6.) If you remember which pin gave you the most problems, push that one down first, applying a fair amount of pressure on the center fan, ensuring your keeping the HSF flush with the CPU, while pushing the pins in.
7.) Its usually best to verify that the HSF is on properly by looking at the back of the MB, but some people just don't wanna go through the hassle of taking everything out. But it should look like:
If all else fails, then I'd recommend you get yourself a 3rd part HSF.
I would check a few things first. Like mentioned, make sure that if you have a push-pin setup that they are all secure. Also, make sure you didn't apply too much thermal paste or too little. Too much can act as an insulator instead of a conductor. Make sure you also have a good path of air flow throughout your tower...a fan on the front for intake and one on the back for out.
I would also suggest a new heatsink and fan. The stock one is ok, but much better can be done. I personally have the Zalman 9700 and absolutely love it. With that, my 9550 is at 29, 29, 31, 30 respectively.