You are correct. Using Ghost from within WindowsXP will make Ghost edit the boot.ini and perhaps even edit the MBR.

Boot with the Knoppix CD. I use cheatcodes
Code:
knoppix 2 vga=normal
but you can boot up however you see if. Gain root access
Code:
su -
Mount the Knoppix HD install partition (I will assume it is /dev/hda3)
Code:
mount -t ext3 /dev/hda3 /mnt/hda3
Run lilo with the following extensions to put lilo back into the MBR as you bootloader.
Code:
lilo -v -C /mnt/hda3/etc/lilo.conf -r /mnt/hda3
If that was successful, unmount the Knoppix HD partition
Code:
umount /mnt/hda3
Then reboot the PC from the KDE menu or use the command:
Code:
init 6
If the MBR and the partition tables is totally trashed then a program that is included on the Knoppix disk, gpart http://www.stud.uni-hannover.de/user/76201/gpart/, can be a real life saver.
If anything goes wrong, either me or someone else can help you.
James