What I think that causing the issue is that you using a cheap chinese breakout board which has TTL buffer ICs on the inputs and requires separate power on the primary side (e.g. a USB connection or external 5volts).
And the designer of that board put TTL buffer ICs on the outputs for the step/dir signals to the drives, but did not place any pullup or pulldown resistors on them.
So, what happens is that if you unplug the UC100 then the primary side of the outputs on the BOB goes into an undefined voltage state, because it is connected nowhere and so the output of the buffer will randomly move 010101 etc., this gives the step signals to the drives. And this is a problem with cheap chinese BOBs and not with the UC100. The UC100 can not solve design issues of the BOB, if you will disconnect the UC100 totally then this issue will likely still happen, so you will see that it is not a UC100 problem.