Ah, why didn't you say Cool n Quiet? Something a little lost in translation I think. CQN? CnQ!
I doubt very much that this is causing the problem. I have Cool n Quiet turned off on my rig and do not experience any adverse effects.
However, AHCI is proving difficult and I don't believe replacing your hard drive will make any real change, but I am prepared to be proved wrong. I am using Western Digital Black 640 Gig SATA3 6G/bs hard drives and I still have BIG issues with AHCI and, when I try to implement it, my system goes from being rock solid in IDE Mode to constant hangs, crashes and other problems with AHCI.