Hi diyengineer,
You should really reconsider your EStop. At a minimum, EStop should kill power to your servo drives. You shouldn't trust anything short of a mechanical switch to stop movement. Killing power to the motor drives is the only safe thing to do.
With that said, I noticed in one of the videos that showed the SmoothStepper's data monitoring screen, that the EStop flag was checked. This says that the SmoothStepper thinks the EStop is asserted. In Ports & Pins you showed it as being Active High, which means the EStop needs to be at +5V in order for it to be in EStop. I would go straight to the source and use your volt meter to measure the voltage on pin 10 of port 1 before and after. You must release the EStop in order for it to get out of EStop. Otherwise Mach will stay in that state. If the EStop button is released and the voltage on that pin stays stuck high, then there is a problem with the breakout board. This is an input on the SmoothStepper, so it is unlikely it is causing it to stay stuck.
Greg