Is their another config file besides usr/share/xresprobe/xorg.conf and etc/x11/xorg.conf that I would have to edit to get my screen to show a proper 1280x1024 view. As of right now it does 640x480@50hz and 1280x1024@50hz but when I select the 1280x1024 my screen gets so big that I have to hit the corners with my mouse so it can pan over to see the full image. I do have an nvidia card with a dvi output, which I just connected yesterday and it work fine until I changed the visual affects in the appearance preferences to "Extra". Now even after changing it back to none my resolution wont set right.

If you're using the proprietary nvidia driver, run nvidia-settings as root and see if that helps.