well after a bit of head scratching I see that the nvidia graphical interface will no longer save what you want to set it to, that is things such as display size, resolutions and such. Apparently this is intentional. I had thought that in the older versions I was able to save this right from the graphical interface, but now I was not able to do so. This is what I did to work around that,
Log on as root user
nvidia-settings (this will run the nvidia x-server graphical interface as root)
apply all of your settings then click on the box that says
"Save to X Configuration File" (this will save for next reboot)
If you run the nvidia graphical interface from the Applications>System Tools> nvidia Display Settings menu and try to save it will produce an error and load the original x config file in and none of your changes will be saved for the next reboot.