Mike,
As someone else said there isn't anything on the BOB that could create that much damage. I would look at the stepper driver especially the wiring. Ethernet cables are used to interconnect the BOB and driver but ethernet cables come in two flavors, one swaps some pins around instead of going straight through.
I noticed in one of the photos the middle stepper drivers is installed upside down as compared to the other two... double check your wiring, it will be reversed right to left from the other two.
I don't have that driver here but I looked at the data sheet. There should be nothing present on the port that interfaces to the BOB that generates any voltage. It is actually optically isolated. Maybe take a peek inside it to make sure a screw or nut didn't fall inside and short something.
Switching to another stepper will not likely correct the problem since in a working driver it is completely isolated from the BOB. In addition swapping to a different motor with different torque curves and inductance will change the maximum speed the motor can move at and how quickly it can accelerate. Ideally you want all three axises to respond the same but often the Z axis is slower than the other two. Changing the motor could get you to a point the machine will need to run slower to compensate for the mismatched motor. This will become apparent when milling circles or other profiles.
My gut says the driver is the cause but I'd double check the cabling first. Disconnecting the cable to the BOB you could power up and check voltages at the driver terminals normally connected to the BOB. None should have AC voltage and probably all should have 5 volts DC or less on them.
Charlie.
Charlie.