The common thing to kde and gnome 3 is composition. Is it possible that xinerama and composition are not compatible. I also think that there are additional things in KDE and gnome 3 that are not compatible with xinerama on multiple GPU. When I disable composition I get different sets of problems. The nvidia driver has also some issues. I do not understand why the nvidia driver in windows works with no issues, but in linux it is missing some things. There was never a nvidia driver in linux that worked without issues as the driver in windows.