Louisssss there are two reasons you will observe the temperature delta.
The first is the one highlighted by posters already...namely inefficiencies in thermal transfer to get the heat out of the chips under the IHS.
As this involves inefficiencies in thermal transfer, anything affecting the uniformity of thermal transfer will also effect temperature deltas at the cores. These uniformity issues can be rooted in non-uniform thermal paste thickness, IHS coverage, IHS flatness, HSF flatness, etc, etc.
The second reason though has to do with the heat generation itself. The most uniform thermal transfer system in the world can't change the temperature delta if one core (or chip for a quad) pumps out 2X the heat as the neighboring core or chip under the same IHS.
In this regard a temperature delta can actually be an indication of the efficiency of the chip/core in question. If a chip creates more heat output than a neighboring chip then that chip will operate at a higher temperature than the neighboring chip.
For example I have a G0 Q6600 that ran at a ridiculous 8C temp delta between the two conroe chips when fully loaded with small FFT. Even at idle there was a 5C temp delta. This was with a Tuniq120.
I tried AS5, TX-1, TX-2 and ceramique. Multiple times each. All to no effect on the temp delta. I tried another Tuniq, another motherboard. No effect on the delta. I even lapped the IHS and the HSF...still same 8C delta at full load.
My conclusion for this chip - thermal transfer inefficiencies are not the cause of the temperature delta, one chip in my quad simply converts more power into waste heat than the other.
Other quads I have with temp deltas were clearly thermal transfer limited as lapping or merely reseating the HSF eliminated all but 1 or 2C of the delta.