Cores can also run very different temperatures due to variations in the calibration of the core temperature sensors.
Also, even the slightest difference in contact pressure of the HSF on the surface of the CPU can cause temperature differences. If you're concerned about it, try reseating the heatsink yet again, and be sure to tighten each bolt exactly the same amount, or as close as you can. Be sure to tighten one, then tighten the one *across* from it (not next to it) and continue around slowly tightening each one a little at a time. Sometimes it can take several tries to get a good seating for a heatsink.