I haven't got a fix for you but I will say that you are not imagining things. lol
I installed 12.6 a few weeks before this new beta patch came out but didn't use anti-aliasing at all with CloD as I was flying with my monitor's native resolution.... but before the alpha patch, with Catalyst 12.5, I was flying at the lowest resolution possible and found that the morphological filtering & AA was working so well that it almost looked like I was running in native.... even gave me a performance boost for some odd reason.
Since the new beta, my performance has been awful so I've tried to go back to lowest resolution..... only to find the catalyst AA doesn't do anything now and yet it seems to work in other games.
High weirdness.
Further evidence of dark occult forces at work?
This game be cursed, I tells thee! Cursed!