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I was thnking the same myself yesterday when I was stress-testing. Coretemp always reads a few degrees lower than TAT. I think I read somewhere that one measures the temps of the die, which will always be hotter. I could be wrong, though.
 

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Speedfan gives me three readings, two "Core" readings, and a "CPU" reading, the CPU reading is always a couple degrees cooler than either of the cores, so I think they measure each core, and one outside the core, like in the IHS, or on the PCB side.
 

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They aren't all measuring the exact same thing. As long as changes to your system (like getting a new CPU cooler) make about the same difference for all three readings, then you really shouldn't care all that much.
 
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