Yep. That was the link I meant to provide. The heat transfer from heat generation to leaving the case is actually very simple.
Steps:
1. Heat generation inside CPU
2. Heat transferred to heat spreader(if CPU has one)
3. Heat transferred from heat spreader to heatsink. This is improved using CPU thermal paste to improve the transfer surface area.
4. Fan blows heat over the heatsink fins transferring the heat from the heatsink to the air.
5. Case fan blows hot air out of the case of the computer.
There's alot to this series of steps. Generally if any of these things goes wrong(except one) you'll know damn well what's wrong. CPU fan stops spinning, case fan fails, heatsink fins bent to heck and you'll KNOW what to fix. On the other hand heatsink thermal paste is one of those things you can't check to see if you did it right. If you do it wrong your punishment is high CPU temperatures. Everything will 'appear' right, but something will definitely be wrong. You can't check if you did it right, because if you remove the heatsink and say 'yeah.. the thermal paste was applied correctly' you now have to clean the surface and reapply new defeating the reason to find out.
Fortunately for heat transfer, the design of all of the components used are effective at transferring heat. The only variable that can't be accounted for is human error. There is the likelihood of poor design to be human error, but this is quite unlikely considering the millions of products that are in use currently proving this system works. The VAST majority of human error will be done by the system builder. Why? Because there's no school to install this stuff correctly. Few people have the knowledge to be able to explain the entire heat transfer process in mathematical detail and why we use so little AS5 and how the heck AS5 works and why. Pretty much everyone that 'knows' how to install CPU/heat sink/thermal paste knows because they've done it 'that way before' so they just keep doing it that way. Others use the manual. Me, I ALWAYS look over the manual while building the system. Sure I've built more machines than I can count, but I still do it. Why? Because I want to see what the manual recommends for installation to see what's different from what i'd 'normally do' just in case there's something I need to know. It sucks building a system completely to have it not POST and the resolution is to take it out, tear it completely apart and start over.
So I'd bet that this problem is human error. Your 2 most likely culprits are the thermal paste wasn't applied correctly or your heat sink isn't mounted to the motherboard correctly. I despise the Core 2 Duo retail box heatsinks. When I installed the first one I had to check VERY carefully to see if it was installed correctly. In fact, it wasn't and I had to pull it off to reinstall it because of the screwed up tabs used. Lucky for me I am familiar with heat transfer physics, so it was easy for me to understand that it wouldn't work as I had it installed and fixed it. But I don't know if I had shown it to some stranger(especially someone building their machine for the first time) would understand the tabs and what is and isn't right.