Did you use Thermal paste? Have you gotten your Heatsink on right? Is the fan on the heatsink running?
Those are just a few things I could think of. To isolate the issue, try running the system with the case side off, turn off all of the case fans, and just let the fan on the heatsink run. The key is just to make sure you've got good, even contact, and a thin layer of thermal paste between the CPU and the heatsink. If you didn't replace your CPU, be sure to clean the old paste off the chip, and reapply new thermal paste.
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