i'm no pro at case fans, but i'm just curious... are you using 3 or 4 pin (PWM) fans?
also, do you have options in the BIOS to tell the board whether each fan is 3 or 4 pin?
if i recall correctly, the third pin on a case fan is for feedback of what RPM it is running at, and pin 4 (only newer fans) will allow the motherboard to adjust the fan's speed, to slow it down or cut it off when things are cool, and rev it up when things start heating up.
can anyone expand on that? i'm curious myself.