Try using a different disk. I made a system 6 bootdisk using my vista computer that my Macs could read when booted into their OS from the hard drive, and everything looked good, but they could not boot from the disk. I made copies on other floppys, and they work.

Also, last semester I had a Classic and an SE/30 at school, and neither could cooperate with disks. My vista computer liked both of their disks, but each time I tried to make them share HFS disks, they would tell me initialization was necessary. Finally I found just one disk that they could both use without reformatting. Also, there are disks that my Classic refuses to initialize, but the SE/30 does and vice versa. So I am learning to simply try many disks. I know its an amateur answer, but it helped my headache a bunch. And try disks from different manufacturers.