Re: nvidia-setting and glxgears
The settings in nvidia-settings are not applied until the utility is run. Hence, you have different settings in the utility as compared to your xorg.conf.
The reason you get ~60fps is probably that nvidia-settings enables sync-to-vblank, which is a good thing. It removes tearing, and there's no need to render more frames than can be displayed on screen.
Use the -l option to load the settings in a startup script.