I found the "B" wire loose at the servo motor terminal strip. However, once I landed it, and tried to reset the drives the Y axis still moves in the same direction however only a 1/4 inch at a time. Short movement, pause for one second, moves again, etc.
I tested and found 5V, ground, and 5 V pulses while moving the motor by hand. I suppose I will swap the A and B wires next. Not really sure why it would respond this way if they were swapped though?