Comment 22 for bug 1002641

I'm havving allmost the same issue on fresh install of 12.04.
Using nvidia-settings I selected "Separate X Screens", saved xorg.conf and rebooted. After I logged in my secondary screen looks like a default X session. A black X as mouse pointer, white background, no menu's. I can't do anything on the secondary screen except moving the X with my mouse :)

My guess is that the "Separate X Screens" option in nvidia-settings works for gdm and isn't available (or not yet implemented) in lightdm. I havn't tested this yet, but switching back to gdm should give you separate X screens. Dunno if this impacts Unities behavior.

Would be nice to have this in lightdm too.