I don't much like ATI/AMD but try to make it a single desktop and see if that helps any. If AMD is anything like Nvidia, the "two desktops" not one single one is killing the FPS. This is not an ideal solution but should help out a ton.

So, instead of "spanning" - make one huge desktop. I don't know what AMD calls it - there is another forum post here about it, search for it as it explains AMDs stuff better.