I had the same problem with being unable to right-click on my desktop after writing out the xorg.conf file via the nvidia X server settings (using Ubuntu 10.04).
I had to manually edit /etc/X11/xorg.conf to get the right-click working again on the desktop.
Here's what I added.
Under Section "Screen":
Option "AddARGBGLXVisuals" "True"
After adding this and rebooting, I'm now able to right-click on the desktop and get the pull-down menu.



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