From what I gathered, its not just that he can't reprogram, its that some buttons aren't showing up. Really, kudos to you for helping Andy, but this is a mess. It could be the adapter that is screwed up, or maybe even the controller. Even if you could reprogram them there could be an issue with the adapter not playing nice with the Jpac, or maybe even the 360 itself having issues since they only recognize signed devices.
Really, I don't get the "easy to switch out" thing. All CP's are pretty easy to switch out, it just a matter of unplugging a couple of disconnects or screw terminals. What you have here is a jamma harness connected to a PC device, that is being converted to a Playstation 2 device which is then converted to an xbox 360 device. I guess I could understand if you wanted to switch between some jamma boards and an xbox on the same cab, but that is not the case here, he's not using a jamma board and is using a TV instead of interfacing with a monitor.
Reallly it seems that all this is being done just to avoid rewiring the CP.
Nobody cares how you interface your machine, it is just sort of mind boggling as to why you would make something so difficult when there are numerous, simpler examples that are easy to follow. All of the "why don't you just use 'x' suggestions isn't people being butt hurt, its people trying to help you out. If you had just hacked pads, or replaced the buttons on a 360 joystick, or something like that, it would take maybe an hour and you would be up and running. You are just adding complexity with no added benefit.
Anyhow. Good luck, I hope you get it up and running, there are a TON of fun xbox games to play on a cab, I am glad I added mine to my cab