I ran RMClock and it was showing Core 1: 30 degC, Core 2: 39 degC...
After several minutes the core temps had fluctuated a few degress but always with 9 degrees difference.
Are the cores laid out sid by side or sandwiched one on top of the other? If they are side by side then maybe the HS seating could account for a few degrees difference but not 9...
I've got an AC Freezer 64Pro and have kept the original TIM. The HS should be in pretty good contact as paste squeezed from all four sides when I clipped it on and the clip was pretty strong. I even gave it a little rotational wiggle when it was in place to ease excess paste out from the join.
The ASUS temp monitoring util reads around 38-40 which ties in with the higher core reading so that in some ways validates the readings and may be able to discount software variances.