It is common that the curvature of the heatsink or processor is uneven, causing those varying temperatures between the 2 cores. For some reason, some seem to be a lot worse than others. I have got a few games open as well a tonne of programs, and my Q6600 (@ 3.0GHz) is running at 36,33,33,35 from core0 to core3.

If you are worried about the varying temps (which I would be if I wanted to overclock), it may be worth lapping the heatsink and CPU with a variety of sandpaper. In fact, would you mind telling me how you applied the thermal paste, and what type it is? You should have followed the arctic silver technique which says put a very thin line vertically across the cores - instructions. If you manually spread it with a card or your finger, that may well be why the temps are so different.

Other than that, nice setup .