well, let me explain something...
before using NH-U12F, I was used Ninja on Opteron 146.
when getting the NH-U12F, at the same time I got myself X2 3800+ E4 (not that one from elhh82's bulk), when prime the proc, I got something temp. diff. both core around 8-10'c but for idle, the temp. diff. both core are indentical, 36'c/38'c. I re-install the HSF and same result obtained.
after getting X2 3800+ E6 from elhh82, I moved the E4 to my another amd rig, and run it together with thermalright xp90c. this time the emp. diff. both core is with 4-6'c which is normal for most X2 proc. this prove that the proc is normal.
okay, then I install the x2 3800+ E6 with the NH-U12F, under idle condition, the temp. diff. both core at least 9'c or higher. while priming, it can go up to 12'c temp. diff. both core. I removed it and installed again for 2 time, the result was same.

p/s: I tried the hsf in both vertical and horizontal location, same result was obtained and noticed that vertical give rise to the PWM temp.
That's a bit funny. I wonder how the core temperature are read. Could it be because of your mobo reading the wrong temperature?
Anyway, saw your sig. 3800+ @ 2.7 Ghz!!! Cool! Is it stable? Vcore from CPU-Z?