If it's anything like my state inspection they connect the machine into the OBD2 port which looks for Powertrain DTC's and checks to see if the emissions monitors are complete. That's why i asked if a standard OBD2 code reader would connect as many have a "state OBD check" function that will tell you if you pass or fail. Would be a clue if this is an equipment issue, or something going on with the vehicle.
Based on what you've posted, I think they are having trouble communicating with the OBD2 port. This is a pretty straightforward, routine task, so I'm going to assume this is a vehicle issue that should be handled under warranty.