sounds like a possible ground loop somewhere.
I would first make sure (with a test meter) that the USB cable shield and therefore the UC100 is NOT connected to the machine ground at all, this should only be grounded by the PC - do this with all other wiring disconnected.
Now connect the UC to the BOB - the same condition must exist.
Now designate a point on your chassis as ground - this will be you star grounding point. The shields to the motors will connect here but NOT at the motor ends.
Connect the shields (if any) on the limits cables here too, but not at the switches.
connect the 5v supply to the BOB (power off), the USB shield must still be isolated.
At this point you have TWO systems of grounding - the control side (PC,USB,UC300) and the power side (BOB, MOTOR CONTROLLERS, MOTORS)
Imagine it as two circles - control and power, now each circle can be connected to supply ground and no problem as no loop is formed, but let the two circles touch (say by connecting the BOB to ground) and you now have a full loop and issues will arise
That should remove any ground loop effects, of course whether it makes a difference i dont know its how i wire my stuff