Yeah, I had this happen to me on a desktop a while back. Somewhere along the way, your lilo got messed up. Probably because you did the install, but didn't want to (or forgot/skipped) install lilo when you did the general installation. Now, Lilo's looking for the kernel and system maps it expects.
First stage boot loader has been able to load and second stage has been loaded but can't execute it.(geometry mismatch or /boot/boot.b has been moved without running the map installer)
I'm not sure why your cd won't work, and have to agree that something might not be setup right in your bios. If you don't get to the MBR on the hard drive (which you wouldn't if you booted from cd) there's no way for Lilo to have a problem. Neither Linux or Windows mess with the bios in this fashion.
Once you do get that figured out, you can reinstall, or it might be easier (and more educational) to boot knoppix or whatever, mount the partition, then "chroot /mnt/<whatever your mountpoint is>". This will "change root", meaning your partion will become the active Linux version instead of the Knoppix version. Then, simply check your /etc/lilo.conf to make sure it's modified and correct, and run "lilo" as root to install the new bootloader.
Hope this helps.