It seems I found my answer! Now to figure out how to fix!
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Many (perhaps most) A4000s were shipped with improperly-wired floppy
cables. These cables had wires 3-5 twisted, instead of wires 4-6. These
cables will work fine for a single drive, but will not properly connect a
second drive. To use two drives that are both jumpered the same, the floppy
cable should have both wires 4-6 and 10-12 twisted. A cable with wires 4-6
twisted will require the drives to be jumpered as DS0 and DS1.