I take it that X windows worked OK when booted to cd? If so read on...Sometimes you just need to copy XF86Config-4 from the cd to your hdd install. It's quite easy to do:

boot knoppix like normal.
I'll assume you installed knoppix to /dev/hda2
sudo mount /dev/hda2 /mnt/hda2
sudo mv /mnt/hda2/etc/X11/XF86Config-4 /mnt/hda2/etc/X11/XF86Config-4.orig
cp /etc/X11/XF86Config-4 /mnt/hda2/etc/X11/XF86Config-4

Do not use the desktop icons to mount your hdd. Do it by hand.
done
reboot