For #1 - are you meaning the game engine slows down? If its a new system then my first check would be to see what the IDE Controller in the Windoows Device Manager is set up as. Sometimes the older generic drivers can cause the data flow across your hdd/cd drives to be jumpy - and hence when fs2 (or any other game) calls for data it doesn't get it as a constant stream. (Especially if its a VIA m/board)
Or it could just be there's some funky resource eating app running in the background.
As for #2 I agree with IceFire, I've not got anything that does full-screen aa but I've seen it happen.
Hope this helps