Hmm... I thought that newer nvidia drivers did the screen aligning automatically? Apparently not.
Well, you can set the horizontal and vertical refresh frequency in "dpkg-reconfigure xserver-xorg" advanced monitor settings (or by directly editing /etc/X11/xorg.conf). If you know the refresh rates that your monitor's manufacturer recommends, that should help you a lot. If you've lost your monitor's manual, try searching the monitor manufacturer's website or do a Google search for "horizontal", "vertical" and your monitor's model.
You could also try opening a terminal window and starting xvidtune from the command line. If you can align the virtual screen with the physical one using xvidtune, you can then press the "Show" button in xvidtune and it should print a new modeline for your monitor in the terminal window. Then you can copy & paste the modeline, adding it under the "Monitor" section in /etc/X11/xorg.conf. Here's an example:
http://www.linuxquestions.org/questi...d.php?t=207579
After editing /etc/X11/xorg.conf, exit from GNOME to the login screen. Then press the Ctrl-Alt-Backspace keys simultaneously to restart X.org and then start GNOME again to see if there's any difference.