How do the other two fans plug in? Do they plug into headers on the case? If so, make sure that you plug the third fan into the third header.
P.S. AMD's Cool'n'Quiet technology is a feature of their 64-bit line of chips that allows the CPU to cycle down when it isn't being pushed hard in order to concerve electricity and reduce heat output but quickly speeds up the chip when it is put to full use. This feature has nothing to do with case cooling.