Top suspect for flaky command operation is the R2LC, consider swapping with a known good one and then reprogramming the engine and see if that helps. Since it works in conventional, that seems to be the most likely.
However, let's try to narrow it down.
If you reprogram the ID, can you use AUX2 to toggle the lights or operate the couplers? If not, that points to antenna or R2LC. If all that works, and it doesn't move, I'd be looking at the cable between the motherboard and the DCDR (motor driver). If you need a DCDR, I'll give you one, I have a few from upgrades that I'll likely never use.
