First, my CPU fan is the Arctic Cooling Freezer 7 Pro Rev.2 .
I run the Intel Extreme Tuning's cpu stress test, the cpu temprature gradually went up from 27c to around 67c - at that time cpu fan speed kicked in at 700rpm. I noticed that the CPU temparature stopped increase and stayed at 67-68c.
So it looks like at boot time the fan speed is around 880rpm but the BIOS reported 0 rpm and the fan speed increase when temperature went up, but the bios only took the readout when it passed certain threshold (in this case 67c)
I also tried to connect the cpu fan to the rear fan header, it did read 880rpm at boot/idle - So just the cpu fan header that reads 0rpm at boot/idle.
Hmm, I am kind of okay with this - Now if I can find a way to disable the alert message about fan has been removed and check your chassis. Anyone knows how?