It sounds like you replaced every part of the setup:
- State machine
- PC
- Cables
- Port
- Port PCB
I could imagine an issue like this being caused by a bright source of infrared light pointed at the setup from above or below. That way, even when the beam is "blocked", IR from the second source can get through to the sensor, making it appear non-responsive.
Other than that, do you have a rig that does work? If so, swapping these parts one at a time into the working rig can constrain the possibilities.
Josh