Hello,
 
I have a Q6600 running at 2.7Ghz with stock heat sink fan. The MSI motherboard utility detects the CPU temperature in the 30-35 degrees range. But after using Core Temp my PC temperature reads at 60, 57, 51, 56. Which of the two reading is the correct one? Also, what alarms me is the big difference in core temperatures.
 
My question is: What is the average core temperature differences of a Q6600?
 
Thanks in advance.

Having four cores is going to give you four different temperatures, the 60, 57, 51 and 56 are all core temps. The 30-35 degrees is the IHS (integrated heat spreader) temperatures that surrounds the out side of the processor. Never use mobo utilities, there always off by too much. Just stick with Speed Fan and Core Temp, btw you temps are fine for using to stock Intel heatsink fan. There is no average core temperature because not too many use the stock HSF. Just don't try overclocking with it!

I understand that 4 different cores would have different temperatures. But why such a big discrepency between core 1 and core 3 temperatures? Is a 9-degree difference in core temperatures normal? Should i reset the heat sink fan?
 
Thanks again.

I've got the same prob too, but I'm using C2D. Sometimes the difference is   up to ~6c. Is this normal for a c2d?

Normally it has to do  with how tight each screw of the heat sink is, but with the stock intel HSF there is no way to adjust it and for the same reason it shouldn't be a problem. Check if your heatsink is locked firmly in every corner. You could also try pressing the HSF hard with your hands during a Prime95 session with 4 cores loaded and hold it there for a few minutes, in order for the stock thermal paste to spread evenly.

I had a similar problem with my e6600.  I was using an aftermarket cooler (TR-u120 Ex) and I was still getting a reading between 4-6 C.  I determined it to be the uneven surface of the cooler and after I lapped it, the temps were within 3C of each other at all times.  You probably don't want to waste time lapping the stock cooler but that could be where the problem is.  

Its most likely the DTS (digital thermal sensor) itself thats a bit off, I do know a way to bring them closer but you may not want to do it. Lapping both the HSF and CPU, let me tell you that Intel processors are NOT flat by any means. Intel processors are concaved high around the edges and dip in the center that might have uneven contact with your HSF, lapping fixs this as close as to 2-4 deegrees difference between all cores.  
 
Remember that just like multiple processors from the same batch won't OC the same, the same is true about the seperate cores. Ever wonder why your OC hit the limit, the weakest core of the four is the deciding factor in how far you can push these processors speed limits. The weakest link applies here, I suggest that you lap both or forget about the differences, because you can reseat your processor 100 times and still get the same result.
 
 
This is what my processor looked like after I was done.

By systemlord at 2008-02-05
 

By systemlord at 2007-12-09