If your PC still thinks it has to boot off IDE it will ignore any bootable partitions on SCSI drives. You still have an IDE drive installed? If you add or remove a SCSI HDD it can also change which drive is sda.
Also, what is it not doing? Do you get an error trying to run lilo or does it just boot with the old kernel even after you execute lilo and reboot?
I'm not really sure what's going on but hopefully something there helps you out, if not post more info. I dealt with all kinds of oddball SCSI boot order sctuff and my current firewall, due to BIOS limitations, boots off the MBR on an IDE drive to access my root linux partition on sda2 and it's onboard SCSI!