The problem is rooted in the way twinview works.
Because twinview fools your os into thinking it's just a double wide screen (in my case 2560x1024) Any applications that load would span both monitors, without really knowing you're running twin monitors.
So twinview fakes standard xinerama hints to your window manager and to apps. However certain apps are coded to over ride certain window manager hints, which in turn can either make the app work correctly, or incorrectly.
Blender for example is coded to hint the WM to get rid of borders and to go full screen. It works great for my purpose of dual screens.
Mplayer or full screen games get the impression from X that you've got one double wide screen, so the app nests it's self in the center of the two screens, thinking that it's only one. This is a feature believe it or not, but it's rotten one if you've got two screens.
Mplayer for example runs full screen borderless across both screens.
As of right now, the only thing you can do is create a seperate config file, or seperate layout and just restart your x-server everytime you want to play a game, or watch something.
It's quite a pain, but there's currently no way to have an app communitate with the drivers to say it wants to be on one screen, not both.