Or the pulses coming out of the g251x board?

I don’t think that checking the pulses will be of any help to you. Mach3 will output exactly the same number of pulses and type / quality of pulses for a +100mm move as it will for a -100mm move the only thing that changes is the active state (logic) of the Direction signal.

If Mach3 drives a stepper in one direction then (within the limits of my knowledge) it will drive it in the other direction unless…
The motor is incorrectly wired or otherwise bad.
The stepper driver is bad.
Mach3 has the step pulse width set incorrectly and or the Step Low Active state set incorrectly (both of these settings are to match the requirements of the stepper driver).
The Mach3 Motor Tuning Velocity and Acceleration settings are set far too high.

If Mach3 had a corrupt installation or other factors were set incorrectly then the stepper motor would not turn correctly in the one direction.

Tweakie.

Quick update.

I bought a new motor driver CW5045 to try. It runs perfectly at less than half the price of a g250x. Problem solved but I still don't know why the 2 new gecko modules were not working. My advice is to avoid the pain, stress and tears and get something else.

Thanks so much Tweakie.CNC.

I am pleased that you found the issue and have it sorted 

Tweakie.