Test each motor individually on a known good output.
@Phantomm thanks. Yes, I’ve now tried that as per @LarryM’s suggestion. I swapped the X and Y axis controllers at the GShield.
Having done this it would seem that the Y-Controller is the issue.
When I wired up the X-axis controller to the Y-motors, the Y-axis had no problems. I can now move in both directions.
But when wired up the Y-axis controller to the X-motors, I had the same issue as before: it only moves in one direction.
I guess the question is WHY?
So if you hook up the know good X-motor to the Y-driver it would still only move one direction, right?
Then “why” are electronic gremlins… 
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Yeah. I wonder if I need to order a new GShield. Might be the solution.
Before I do that, would there be any other reasons? Like firmware or another wiring issue?
Basically the Y-driver only wants to give out a signal for one direction; no matter which way you jog it.
I can only guess but it is possible that the driver is actually okay, receive all step commands but all in one direction. If so it could be down to a bad chip.
I would advice getting a new Ardunio and shield, or better yet a new Ardunio and 4 individual drivers aka TB6600. It will be better in the long run.
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You have a bad driver chip on the gShield or a problem with the Arduino.
If you are going to stay with your current electronics I would replace the gShield first and see if that fixes the problem.
Thanks @LarryM
I happened to have a spare Arduino. So I tried that, and had the same issues.
This would lead me to believe that the problem is with the GShield.
Weirdly enough, I got it working the way is it should for about 10 seconds.
It was after a I tried switching the Arduino (which had no affect). When I reseated the original Arduino and pressed the reset button on the Arduino, it was possible to jog it in both directions.
But as then I unseated the Arduino in order to screw it into the control box. And when everything was back together again, it was back to the original issue.
Weird. Any thoughts?
Poor solder / socket connection, could also be a poor copper board joint somewhere inside the GFK sandwich.
I really suggest you change them as the trust level will be poor and replacement is cheap.
You could try cleaning the pins that go between the Arduino and the gShield. Use a regular pencil eraser (the pink one) and burnish the pins to remove any built up corrosion.
Since the Y motors are mounted opposing each other one has to have wires switched.
I believe it is the green and black or green and white.
Assembly instructions clearly stated that when I assembled mine.
The wire switch is at the X-controller terminal, not at the motor.
The OP already have both motors running the same way (in unison) so no need to swap any wires.
Wether OP jog in Y+ or Y- direction, both motors only move the gantry in one single direction.
My understanding is that it could be anywhere. Here is what he originally showed.
Both Y motors looked to be wired the same end to end.
OK now I see it, the wire colors are different on the jumper cable between terminal blocks.
That’s true, but my comment was in keeping with the instructions and trying not to have people confused.
Understood.
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Yes the red wire on one Y goes to the blue wire of the other Y.
Possibly. Where would this misalignment be? I had wondered about this also.
Each driver on the gshield has two input that come from the arduino. A step pin and a direction pin. It sounds like the gshield isn’t picking up or properly handling the direction signal. If this signal isn’t processed, the stepper driver will always go the one direction.
I don’t know a good way to test the signal coming from the arduino. If you are looking at buying a gshield, consider looking at alternative drivers.
As some have mentioned, the tb6600 drivers work well. I used a 4 in 1 tb6600 driver that cost less than a replacement gshield and performs much better. I even used my original power supply from the shapeoko 2 days but it doesn’t provide enough power to run the drivers at their full potential. I just keep them dialed back a bit and it has been fine.