TilDeath and I were having similair problems with my 9800GTX. On the EVGA Precision Graphics Tuning graphs, my core clock would drop from 738 to 301. At the same time, my in game FPS would drop from a steady 59-60 (monitor limit), to in the low 20's and 30's.
I had my screensaver set to turn on in 10 minutes of unuse, and it seems that after being in AH for 10 mins, it would drop the core clock speed as it tried to use the screen saver funtion. After turning that off, it cleared it up for the most part. Now it will be at 301 while on the desktop, IE, etc. but as soon as I start up AHII, it jumps back up to 738 speed and runs fine. I'm not really sure if that was the problem or not, but it did seem to fix the in-game stutters that I was having.