Odd joystick problem with AES w/debug bios

I'm having a weird issue here. I have two Neo Geo systems, four old-style joysticks, and a MAS Neo stick. One Neo system is a consolized 1 slot MVS made by Jeff Kurtz that I recently received, and the other is an AES system with a debug bios.

I have been using the CMVS with the two joysticks that I originally had, and all is well. I just tonight tried using the sticks that came with the CMVS with my AES system. Everything works great in the game, but when I try to go into the debug menu (select and C) everything messes up. It's like the buttons all do the wrong thing. The thing is, BOTH of the sticks that came with the CMVS do this. The two old style sticks that I already had do not do this, and the MAS stick does not do it either.

I did a search, and the only thing I found was this thread:

http://www.neo-geo.com/forums/showthread.php?t=21074&highlight=joystick+debug

Which explains the problem exactly, but there was no solution found. This isn't a big deal since I have enough sticks to go around, but I'm trying to figure out WHY it does it. All the sticks should be the same, and if anything it should have been the MAS stick that didn't work, right?

Is there a reason why you are still running a debug bios and not a Unibios?

I bought the system that way, I believe it was installed several years ago, before the Unibios came about. I'm sure that if the AES had the unibios it would be fine, as my CMVS runs perfectly with all sticks.

My CMVS is using Unibios 2.2.

I figured out what it was when I hooked the joysticks up to my CMVS. The joysticks are modified. When hooked to the CMVS the select button is disabled, but the start button is rigged to be both start and select so it can open up the unibios menu.

That doesnt make sense, why would it be rigged like that?