Ok, I have managed to fix the issues I have had whereby I got better framerates in windowed mode than full screen. In the 3D tab of Catalyst, I changed everything to use application settings, disabled Catalyst AI, unchecked enable adaptive AA, checked the triple buffering, minimap detail level to performance and wait for vertical refresh on unless application specifies.
I have no idea how changing all that affects running the game but I can now run it in fullscreen on max with more than playable frames.
I am surprised that something like that can affect a game so much. I never even noticed that tab before. What is anybody elses settings in there? I use a 4870x2.
Did you try those settings one by one? Perhaps one of them was just the culprit?