This is taken from comments made by jeff.edu for bug 10645 and reproduced in the test lab: "Lilo is unfortunately still not very good at dealing with combined scsi/ide setups. It just blithely assumes the ide disk will be first. If you just add an ide disk to a previously scsi-only system (and your bios is smart enough to still boot from the scsi disk), you are in for trouble. The next time you type 'lilo', it prints the innocent sounding "Warning: /dev/sda is not on the first disk", and then proceeds to totally f-up sda's boot sector (it be set to load linux from the location on hda where the boot file on sda is actually located). It will be a while before you successfully re-boot your system after you do this."
Here is the output from running LILO as described above: % lilo -v Warning: /dev/sda is not on the first disk LILO version 21, Copyright 1992-1998 Werner Almesberger Reading boot sector from /dev/sda Merging with /boot/boot.b Boot image: /boot/vmlinuz-2.2.14-5.0 Mapping RAM disk /boot/initrd-2.2.14-5.0.img Added linux * /boot/boot.0800 exists - no backup copy made. Writing boot sector. % Upon reboot, only LI of the LILO boot prompt is displayed...
I had this problem, when adding an LS120 (IDE Floppy drive) to my system. The only way out for me was to use the rescue disk, re-write the boot sector with lilo and then remove the IDE support (unfortunately) from the kernel.
Unfortunately, there's not much you can do on x86 systems as there isn't a reliable way to get this information