I would strongly suggest to avoid measuring the AC voltage directly. The current is another story - there is a lot of galvanically isolated current sensors that can be directly connected to PoKeys's analog input. ACS712-based current meter would only require a simple voltage divider to lower the voltage from 5V to 3.3V that PoKeys is using.
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.