I have a system with an ATAPI CDROM as hda, an Sparq removable drive as hdb1, and a SCSI drive on sda with sda7 being my root Linux filesystem and sda1 being a Win95 partition. I have LILO installed on the SCSI drive's main boot record and use it to boot either Win95 or Linux. When upgrading from 5.2 to 6.0 the installer only offered me the choices of putting LILO on either hdb1 (the Sparq) or sda7 (my Linux root). I wanted it to go onto sda's main boot record, just like it did before. That's the first problem: I should be able to do that. Not having that choice, I selected sda7 for LILO and sure enough, on reboot it got as far as `LI' before hanging. I fixed the problem by booting from floppy, modifying /etc/lilo.conf and then running lilo by hand.
This issue is fixed in the 6.1 installer.