3dmark06 is extremely cpu bound, but that being said, that is a low score for that setup. What is your cpu score? Run Prime95 torture test and bringup task manager to make sure both cores are running at 100% I'd say with that setup, you should receive a score of somewhere around 9000 - 9500 for your 3dmark score, and around 2000 for your cpu score (there is a cpu chart here at toms, but I'm too lazy to look it up)
AMD cool N quiet shouldn't come into play, but I'd turn it off if I were you just to remove any question as to this being the problem.