The board has an issue where the auto-power-on circuit will not work as intended. When you turn off the power switch on a computer containing the emulator it will power off the BBB. If you turn the power back on before the capacitors are discharged the circuit should force the BBB to power back on.

The error prevents this circuit from working so unless you power off the BBB for long enough for the capacitors to discharge (1-2 minutes) the BBB will not power back on so the emulator will not work.

This is normally an issue when you are using the power switch to reboot the computer. If you don't do this the only change is you should change the power off command to halt.

nohup /root/powerfail/powerfail --powercmd "halt -f" --command "/root/emu/mfm_emu --drive 1 --file /root/emu_file" > /dev/null 2>&1 &

If you wish to fix this the easiest way is to not connect to the board R26 on the side shown in the picture below. Connect a wire from the lifted resistor lead to the pad labeled 12V. I used gel superglue to attach the wire and resistor to the board to ensure they won't move or get snagged. If the free end of R26 gets bumped such that it touches other pins things will be damaged.