I would suggest you to upgrade to 3.1.47 firmware first (the latest available).
Regarding the axis inversion - use the Motor Outputs settings (in Ports & Pins dialog) to toggle the Dir LowActive fields. Although port and pins fields have no meaning for PoKeys devices, 'Dir LowActive' field still does have.
Did you try doing a dry run (without the drivers attached)? Is PoKeys connected to a network or are you using a direct connection with your PC? We executed more than 10 consecutive runs of the same file now and there were no issues.