I just bought and put together a system with a MSI Z68A-GD55 G3 board and an i7 2600k. Everything works great and there were no complications. Fan wise, I have a Skythe Katana 3 CPU cooler, and a big 25 cm fan right on top of the CPU (plus a small one blowing in at the front).
On a cold boot (computer was off for 8 hours, relativ cold room temperatur), the BIOS says the CPU is running at about 45 degrees Celcius. Once in Windows, however, the BIOS tool from MSI says 35 ° C - and I assume it's reading from the same sensors. In theory, it should be the exact same temperature, since the tool is the Clickbios GUI for Windows.
I severely doubt, that the CPU gets colder on boot, if anything it should be getting warmer. I have the CPU fan throttled at 37.5% to keep things quiet, and am quite happy with the temps shown in Windows.
Does anyone know where the difference comes from? Does it have something to do with the way the i7 works (just one core monitored, or the average temp, etc), or the board? Is it a bug? If not, which value should I take for measuring temps?