I've been looking into this as well and best I can tell, the issue is that your window manager (Gnome) uses the xinerama extension to get hints about monitor locations and uses them to place maximized/fullscreen windows. If you can prevent this, you'll get your wish.
In compizconfig-settings-manager, under General Options, Display Settings, disable Detect Outputs and delete any outputs and you should be able to span windows correctly.
Alternately you can try setting your resolution similar to the example. Be sure to remove the example which will be like 640x480+0+0.
The other way involves reconfiguring X to not load the xinerama extension.
Note that the xinerama extension is distinct from the xinerama feature. You'll see in /var/log/xorg.0.log if the extension is being loaded, and you can verify that with the command xdpyinfo | grep XINERAMA.
I don't have the answer for how to prevent the extension from loading, but I was unable to stop this via xorg.conf using the fglrx drivers.