OK -- first-time builder. I think the other poster is fairly correct, but check see if your HSF is properly mounted.
Frankly, even with AMD I wouldn't bother with the stock HSF assembly -- I'd spend $30 or $40 and get one of the recently introduced heatpipe coolers, and use Arctic Silver 5 thermal paste.
One way of testing the processor temperature readings is to get a simple digital thermometer -- LCD readout -- and tape the thermal sensor to the bottom of the Heatsink as close as possible to the processor without allowing it to get pinched between the CPU and the heatsink. The reading will not be the SAME as the processor's own sensor reports in the operating system or as reported in BIOS. The processor's sensor should report a reading maybe five to eight degrees F higher than the thermal sensor wire taped to the heatsink.
Probably -- take a look at the "Cases and Cooling" forum. There are several ongoing discussions there, and people bringing with them problems no different than what you imagine yours to be.