Comment 1 for bug 224845

I have the same problem with a slight different xorg configuration, my xorg.conf has two different Monitor, Device and Screen sections, the first is for the CRT monitor the second is for the TV out.
Nvidia 6600gt and proprietary drivers as yours and I'm using hardy (upgraded from gutsy).
I have noticed that if I start a second gnome-panel by pressing Alt+f2 from the TV monitor, and run a Thunar file manager from there all the applications that I run clicking on a file inside thunar are correctly displayed in the TV.
If I run an icon Launcher form the desktop of the TV the application is displayed in the wrong monitor.
So I think this is a nautilus related bug