I recently built a core2duo system and noticed that one core always has a lower temp than the other. At first I thought it may be the stock cooler but today i installed a Thermalright SI-128 and the 2 cores are still reporting that one is hotter than the other. With the stock cooler I was running around 40-47C at idle with the second core being the hottest. Now it's running at 36-40C at idle with the second core being the highest. I have my 2 front fans pulling in air, the 2 side fans pulling in and the 1 top and 2 rear as exhaust.
Here are some before and after pics.
Here are some before and after pics.