IgnitusBoyone: The SBC has no VGA, hence the serial options in the lilo config. Just for the heck of it I'm going to try adding two options, changing labels, and setting a prompt. Perhaps we'll see something interesting with that. Also, I'm going to let grub give it a go.

In the mean time, has anyone ever heard of a condition where Linux's /dev/hd? is not aligned with the true start of the drive such that lilo is not really writing to the MBR sector?

IgnitusBoyone: The SBC has no VGA, hence the serial options in the lilo config. Just for the heck of it I'm going to try adding two options, changing labels, and setting a prompt. Perhaps I'll see something interesting with that. Also, I'm going to let grub give it a go.

In the mean time, has anyone ever heard of a condition where Linux's /dev/hd? is not aligned with the true start of the drive such that lilo is not really writing to the MBR sector?

OK may be you should try Grub for a change.

First I would put Lilo inside its root partition first. I would forget about the -C parameter as you are using the default /etc/lilo.conf. THus I would make Lilo chainloadable by
Then I shall make a bootable Grub floppy as decribed in Chapter 3.1 of Grub manual. This just an operation to dd the files, stage1 and stage2, into a floppy. These two files are stored in the /lib/grub/i386-pc subdirectory in any Debian that supports Grub. If your Debian hasn't got them (My Woody hasn't but Sarge has) you can "source" them from a Live CD like Ubuntu, Knoppix etc.

If you boot up the bootable Grub floppy you get a Grub prompt. Commands asking Grub to load the Lilo in hda1 are
That to me is a sure fire method to test the Lilo compiled into the root partition of hda1 (inside its boot sector). Grub counts from zero so as hda1 is the 1st partition of the 1st disk it would be known to gRub as (hd0,0).

You can ask Grub to boot the Lilo in MBR with commands exactly as above but with the first line replaced by "root (hd0)" meaning the root is the whole of the 1st disk (hd0) and that is its MBR.

Ultimately you can fire up Your Linux by Grub with these lines
If Grub boots to the old image then you have misled all of us and didn't manage to put the correct version of the kernel in vmlinuz.

I think we are bottoming this one out if Grub is used to give a second opinion of the whole thing.