It sounds like the boot priority of your hard drive is set higher than your floppy drive. If that happens, the system will always attempt to boot the hard drive first. When you're in 1.3, the filesystem expects components that don't exist under 1.3 and you get the errors you're experiencing.
Under 3.x, open HDToolbox and set the boot priority of your bootable partition(s) to 0 or 1. DF0: is always 5, I think. Or maybe 10.
