Have you checked that the floppy cable attaches correctly to the floppy drive itself and the floppy drive connector on the motherboard?
If normal AmigaDOS disks won't boot, then your boot priority on the HD could be set too high, normally 0 is where it should be set. If you set it higher than the internal floppy's priority of 5, you won't be able to boot from the floppy except for non-DOS disks.
Some true, some not true. If the priority of the HD is set to a higher value than the floppy drive, the HD will always be booted as the first device.
If a NDOS disk is inserted, this disk will not be booted either; you will have to enter the boot menu and select DF0: as you boot device no matter if you are using a AmigaDOS disk or a NDOS disk.
