With everything disconnected, and a simple USB cable for power acts the 
same, points in the direction of an over current shutdown due to shorted IO 
on the BBB CPU.  

If you can RMA it and get another, I would try that.

You need to examine your application and make sure that all I/O pins are 
operated within Voltage and current limits, and the inductive "kick" from 
your stepper motor is not getting back, somehow, into the BBB I/O.

--- Graham

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