So i also have a Crosshair III with a Phenom II 965 and i replaced the stock heatsink with a scythe mugen rev B. Got the same error on the boot screen, searched the forums and it sounded like the mobo monitors the fan speed.
Because the mugen is a PWM fan, it can throttle itself back if you don't have it manually cranked to 100%. This can cause a low RPM warning (even though nothing is technically wrong).
So i went into my bios, set Monitor Fan Speed for the CPU fan to Ignore and problem solved.