Could you provide some more specifics. What are you setting it to when you see the issue (Anti-Aliasing 2x)? What are you setting it to when you don't see the issue (Anti-Aliasing Off). And screenshots of the before and after. Getting a copy of your debug.err would be handy too.
For anyone else reading, let us know fi you are running into this.
Sorry Mr Derek, but even though I had NOTHING forced from my CCC, I set it to factory defaults anyway. I also unticked 'enable surface format optimization'
I then set my AA to full in my game and it worked. It would seem that a innocent CCC setting can bugger up the AA in FE, handy for those coming across such in the future. Now it's just a case of discovering which setting it was that caused the problem.