As you have an ATI card have you thought of using the shader 3 mod as that might help you get back some of your performance when you have lots of cloud cover.

http://forum.avsim.net/topic/283701-bojotes-shader-30-mod-for-fsx/

Its a 30 page thread so make sure you read it so you can see its development over time and see if there is any issues you might encounter.

if i had an ATI then the chances are i would use the shader 3 mod. Also are you using fsx or the ati contral panel to set AA within the sim ?