I had a problem with the nvidia-settings tool. It couldn't save to /etc/X11/xorg.conf.
Solution i found here:
remove any old xorg.conf / xorg.conf.backup
sudo rm /etc/X11/xorg.conf sudo rm /etc/X11/xorg.conf.backup
create a new clean xorg.conf
gksu nvidia-xconfig
start nvida-settings a root and now you can save.
gksu nvidia-settings