If the host controller uses TTL drivers instead of the normal open collector drivers it will prevent the MFM emulator from powering down and back on properly. The most common symptom is the emulator doesn't power itself back on when the host power is turned back on after being off for a short time. It can also cause the Ethernet to fail to operate much more frequently than normal (LED's off).
It appears the many Convergent machines use TTL drivers for the disk drive.
If the beaglebone is in the state where it is not powered on but the host computer is on you can verify this is the problem by measuring the voltage from the 3.3V pad P11 to the GND pad P5. If the voltage is greater than .4V this is likely the issue.
The easiest solution is to remove RN1 and RN2. Since the drivers are TTL you don't need the resistors as pullups. The resistors also act as terminators to reduce reflections on the lines. For normal length cables the termination isn't needed for proper operation. I have verified it works fine in our 7300 without the resistors installed.
The resistors can be retained if Schottky diodes are installed between the 3.3V rail and the resistor pack pin 1. This requires cutting the trace and soldering a diode inline. The resistors used for D1 and D3 should work for this though their form factor isn't ideal. For testing I used a 30BQ015 diode I had around. Small signal Schottky diodes may have too much voltage drop. Each line that is low draws around 20 mA. I also cut the trace rerouted the first drive select to unused RN1 pin 6 to avoid having to put a diode on RN2.
I will ship future boards with sockets for both resistor packs which will allow them to be removed if you run across a machine with TTL drivers. I have run our 7300 Unix PC without the resistors and it seems to be working fine.