JohnZS: You could try remounting the HSF but personally, I think the differences you are seeing are all related to sensor error. When you have one sensor reading too high and one too low and the combined error can be significant. I'm prepared today to be enlightened by Intel. I've given it my best shot to convert the sometimes screwy sensor data into some meaningful temperature numbers. Now I'm looking forward to how they suggest doing it.
I wrote a small utility program a while ago that lets you read information directly from the model specific registers within your CPU. If Intel announces some secret info hiding in there then you might be able to use this tool to discover what it is.
http://www.fileden.com/files/2008/3/3/1794507/MSR.zip
The digital thermal sensor data that all programs are using is in MSR 0x19C and is located in bits [22..16]. Avoid clicking on the Write MSR button unless you know what you're doing.