You usually need a combination of Calibration Factor and TJMax correction.
It's not unusual for TJMax to be different between cores. For the 45nm Core 2 CPUs, differences up to 10C between cores is typical. The Intel TJMax specification for your CPU is 100C but the actual TJMax might range between 100C and 110C. This range is my best guess based on the testing I've done. Intel has never publicly documented their calibration procedure so all I can do is guess.
To try and find out how much TJMax offset your two cores have, you need to try and get the cores hot enough to the point where slope error is insignificant which isn't until about 70C. I like to run Prime95 with the Small FFTs option for a consistent load but with an Atom CPU, it might not be possible to get the core temperature hot enough with this test. Try running that test for about 5 or 10 minutes until your core temperature stabilizes. Don't use any calibration factors during this part of the calibration procedure.
The 9C difference you are seeing at idle will likely decrease a little at full load depending on how hot you can get your peak core temperature. If this happens, this is a sign that the temperature curve for each core are at a slightly different slope.