I noticed vista had 2 E6700 and 2 Q6700 installed so i booted into safe mode removed them and restarted but it hasnt made and difference other than device manager now shows 4 Q6700's.
What CPU cooler are you using? What is your cpu cooler setting(if variable)?
I have seen this happen when i was evaluating the right (minimum) setting for my ZALMAN CPU cooler. There are times that the BIOS detects only 2 cores (2 count) when I restart the PC.
It went away when i got the CPU cooler settings right.
Please detail your hardware to get better recommendations from this forum.