Red822 wrote :
... is it OK to assume that maybe the temp diode in the CPU or the sensor in the mobo is shot?
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Regardless of the offset, if the Analog Thermal Diode within the substrate layers of the processor package is functioning properly, then you'll see it scale up and down with the Core temperatures by using SpeedFan and Prime95 Small FFT's.
SpeedFan detects and labels thermal sensors according to various motherboard, chipset and super I/O chip configurations, so the label for CPU temperature (Tcase) might be CPU, Temp 1, Temp 2, or Temp 3. Repeatedly start and stop Prime95 Small FFT's at 15 second intervals, while observing whichever SpeedFan temperature that scales with an Idle to Load Delta similar to the Cores. This will identify your CPU temperature sensor, which is the "Analog Thermal Diode".
If it's working OK, then the problem is miscoded BIOS, which happens all too often, since BIOS programmers must encode each new release with every possible processor variant for a given socket type. However, the good news is that the offset can be calibrated in SpeedFan by using the "configure" button. (See Section 11 in my Temperature Guide). When properly calibrated, CPU temperature should be 5c lower than mean (average) Core temperatures during Prime95 Small FFT's. It'll still be wrong in BIOS, but at least it'll be correct in SpeedFan.
If it's not working OK, then the Analog Thermal Diode is bad, which means your Q9400 is fauly. You can RMA it, or just ignore CPU temperature and use Real Temp to monitor Core temperatures only, which should never exceed 76c. Also, there is no "sensor in the motherboard". There is no thermocouple in the center of the CPU socket touching the bottom of the CPU, and hasn't been for many years, since the erra of the single core processors. Here's how it works in current technology:
From my Core i7 and Core 2 Temperature Guide - http://www.tomshardware.com/forum/ [...] ture-guide
Section 5: Findings
(A) Tcase is acquired on the CPU substrate from the CPU case Thermal Diode as an analog level, which is converted to a digital value by the super I/O (Input/Output) chip on the motherboard. The digital value is BIOS Calibrated and displayed by temperature software. Motherboard BIOS Calibration affects the accuracy of Tcase, or CPU temperature.
Does this help?
Comp