I assume from this statement that you are not using two of the four wires in the cable. It is not a good idea to leave "floating wires" that are not connected, or even to run two of the wires as a parallel signal wire and the other two wires as a parallel common wire.
The motor cables should be four conductor shielded cable, not the wire from the breakout board to the Gecko drives.
Look in my build log for photos of my rewire job yesterday and today. You will see how I rearranged the step and dir wires red and blue doorbell wire and hooked up the motor cables. We'll know soon if it works better. It looks neater anyway.