All the X window configuration is from the central file
/etc/X11/xorg.cong


You can try
dpkg-reconfigure xserver-xorg

from an alternate console.
In non-debian based distros there is xmodelines to generate a modeline at a desired refresh rate, however with knoppix you can try xvidtune from a terminal.

Also have a look at this guide:
http://doc.gwos.org/index.php/ChangeResolution