You do indeed have 2 lilo's. You are certain that your current Linux install is in /dev/hda3? It might be easiest to just reinstall your boot loaders. If you have a floppy drive you can boot a win98 floppy and do fdisk /mbr. Boot the machine- it should boot straight into windows. If so good. Use another floppy to boot Linux OR boot the Knoppix cd, mount your /root partition:

mount /dev/hda3 /mnt/hda3

Change root to your /root partition:

su
chroot /mnt/hda3

Then rerun lilo from there.