This is odd because fsx doesn't really care what your resolution is and you get the same frame rate regardless of rez because the sim is so cpu bound. I get the same fps at 1920x1200 with my 28" as I get with my th2g at 3840x1024. The ati card sure isn't helping you either as any time there are clouds in the sky your frame rate will take a massive hit with ati cards. Wish I could be more help.
Yes, clouds do flicker a bit!
Very strange that you don't suffer any issues. I've even lowered by FSX graphic settings and although the FPS are better they're still no way good enough compared to a single monitor without the TH.