That is odd...I'm assuming you're using an OEM Apple/Adaptec SCSI card with the drives...correct? It sounds like it would rather boot from a drive on the ATA bus, but it's curious that it wouldn't look to the SCSI drives next. Is there a firmware update for the SCSI controller?
I don't know if this works on pre-G4s, but have you tried holding the option key as the machine boots up? Doing this will force the machine to look for evey OS installed and allow you to choose the one to boot into. Again, this may only be a G4 thing, but it's worth a try.
The other thing I'd try is: install an OS on the 60Gb drive, let it boot from which ever drive it wants to then use Start Up disk to force it into booting from the drive you want it to. Dunno if it will help, but again, what do you have to lose?
Good luck!