Having read your very lucid thread NX, despite the obviousness of where the problem lies, people seem to still be focusing on the expression pedal. Too bad you started the thread thinking the problem was with the Expression pedal (which is exactly what I would have done, too). You've clearly stated many times that the problem is with the shortboard.
Perhaps you might want to consider starting a new thread where you state "Line 6 short board is unable to detect an attached expression pedal on startup". Doesn't matter if it is a Line 6 pedal or not. Just say you are using a Line 6 pedal.
I wonder, however, perhaps the circuitry is such that it is unable to process the detection code? Or do you think it is as simple as them rewriting the firmware to add a detection check at the end of boot? If the pedal is already plugged in, maybe they can't run the detection? I don't know, I'm a mech eng guy.
Anyway, hope everyone can see that this problem is independent of the expression pedal that is attached. It's a basic bug/feature of the shortboard itself.
It also seems as though there is another bug as the board is not working as designed, i.e. it's not illuminating both lights even when it knows the pedal is there (I think I got that right). Seems like they should process an update anyway.