I too have this same issue.. I fix it on a permanent basis by doing the following.. I run the nvidia config tool and then when I try to apply the settings from the tool it can't because the /etc/X11/xorg.conf is owned by root.. so I start a text editor by sudo and then paste in the changes that are specified in the tool.. ( There is a button to show you the changes) and then just paste them over the current file and save. This always works.. for me it's just a pain in the behind to do it this way and would be quite a chore for grandma to accomplish.. I wish the nvidia tool would be ran with root privileges. would solve this whole issue once and for all.