I have always noticed a ~2C temp difference with both TAT and Coretemp usually more noticable at idle with my E6600 also. I always attributed this to differences in the temp calibration.
ugh your Core #0 should have a higher temp since that is the priority that the load goes on. that causes the temps to difference in 1-3 max. it shouldn't go over 5. if it does. you got a problem buddy. =] hope this helps.
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