The NVIDIA applet in Ubuntu 9.04 will not write to the stock xorg.conf regardless of permissions set, and regardless of whether or not it’s running as root.
Here’s what I did to get around it:
sudo mv /etc/X11/xorg.conf /etc/X11/xorg.conf.bak
The first step creates a backup of your currently working xorg.conf file.
Step 2 runs the NVIDIA utility to generate a new xorg.conf file that the utility can actually read.
Step 3 runs the graphical NVIDIA setup tool as root, so you can actually save your changes.
If this does not work then after step 1, do sudo rm /etc/X11/xorg.conf to delete your current xorg.conf file. Then run sudo nvidia-xconfig and sudo nvidia-settings.