Alright, figured out the problem was eyesight.
I had put the order of wires on one motor incorrectly, then when I wired up the second test motor I wired in the wrong order again.

Comparing the motor connector to the one that worked showed I had swapped the red and green wires.

Cut, crimped and now in the correct order it is working!

I have just finished wiring up my CoreXY Voron2 and noticed an error in the web panel when I was issuing G0 X10 S0 commands.

Warning: Error: Short-to-ground on drivers 0

Things I have checked:
Swapped the X and Y stepper cables and the error follows the cable showing this error:

Warning: Error: Short-to-ground on drivers 1

I have also verified with a multimeter that none of the wires to the stepper are shorted to ground.

Lastly I have built an entirely separate cable to go directly to the Duet from the stepper, in case there is an issue in the long cable chain routing.
The error persists with the new cable.
Moving the new cable to another stepper shows that the error goes away.

Is it possible the stepper itself is bad?

Update: I have wired in another stepper and the issue persists.
Also, the stepper moves briefly then the error appears and it won't move again.

Any help is appreciated, thanks!