Well it seems to be rather difficult to make a floppy from Knoppix. I don't know why. Anyway..... You can reinstall lilo with the cd. Simply boot the knoppix cd.
Code:
su
mount /dev/hda2 /mnt/hda2
chroot /mnt/hda2
lilo -v
CTRL+D
That will reinstall lilo which should also pick up your windows install.