Just built my computer and first booted it. Processor is i5 2500K, motherboard is an MSI c43 p67 1155 LGA, has thermal paste on it(a pea size spot and then spread pretty evenly) and the stock fans for cpu and case. It's not overclocked or anything yet but when I run the BIOS it says my CPU temp is 95 degrees C, in other words it should pretty much be on fire. It took me a second to realize it wasnt in Fahrenheit so it was on for maybe a minute. Then i touched my hand to the heat sink, its cool, not even warm.
It has to be a problem with my temp reading right? I mean i don't see how it could be so hot and the heat sink be cool and everything running normally.
I wouldnsuggest the same. Download a program like core temp or hwmonitor. See what these say the CPU temp is. I realize you may be scared of the CPU overheating, but it should either throttle itself down or shut itself down before this happens in order to prevent damage.
With what you described, it could be a misreading, but the only way to know is to see what other programs say.
You say you used the stock cooler, did you use the pre applied thermal paste or put your own on? If you put your own pea sized dot on without removing the pre applied paste on the stock cooler you may have used too much and that could be the cause, but I don't see how it could be that high.