If configured as two different X-Displays I won't be able to drag windows across the displays, which is what i want, I thought that was only available in twin view.
Anyhow why does it change, when I enable desktop effects otherwise it's fine. I have a feeling it's because when I'm using twinview the system thinks that there is only one display that is 3200x1600 and not 2 of 1600x1200. Therefore when anything inquires what the screen size is it return 3200x1200 and sets the full screen to be that.
BTW is there a difference between XFree86 and Xorg conf files (since i have the latter)??