Vesc Pronto Hall Sensors not detecting

I bought a vesc pronto a few months back. I just had time now to set it up on my ebike and it seems like the hall 2 input is not working. I tested the motor off the bike with an external 5v power supply and
logic analyzer which showed the 3 hall sensors toggling as I would expect, so I'm fairly certain that the hall sensors are working
properly. I then swapped the hall sensors going into hall 1 and hall 2, given that the hall sensor on hall 1 was showing correctly in vesc tool. After swapping and rerunning motor setup and hall_analyze it still shows hall 2 always high (not toggling). It seems like there is an issue in the pronto itself reading hall 2 input.The one thing I'm not able to test is if it's an issue with the 39 pin
connector not making good contact on that pin. Has anyone had a similar issue?