I'm more familiar with the I-PAC than the J-PAC, but I'll try to help with what I can!!
I've been running MAME off of a Killer Instinct machine which uses the same control panel layout as the Capcom Fighting Games. When I plugged it all in it seemed to work fine for me. Perhaps the harness is wired differently for KI? I don't know, but I don't think so. To me it seems more natural for the buttons to be:
123
456
Like when you read across a page... left to right and then down to the next line. Feels comfortable to me, but I've noticed some of my friends couldn't figure out which buttons to press in games that only took 2 or 3 buttons. Upper left just makes more sense to me.
The real problem here is more generic with MAME. Except for defender and a few other games, MAME defines inputs as P1Button1, etc, while the actual game has labels on each button. If MAME had a input labelled JAB or HIGH PUNCH, you could set this up to match whatever button on your controller and everything would be okay.
I don't think you will ever see this change in MAME and it's not a very big deal anyways.
I did have one problem, though, but it may be my encoder. I have a J-Pac. Anyways, the medium and high kicks (5 & 6) on the second player dont' seem to work right. If you press them individually they don't work at all. Press them both at the same time and both characters kick. I tested it out in notepad to find out what the output was giving me. It had a string of 3 characters, though I don't rememebr what they were. Has this happenned to anybody else? I love fighting games, so I really need this fixed if possible. Is it my encoder or a config setting?? I checked my wiring and it looked good. I have all my wires seperately color-coded.
I was on Andy's site and the JAMMA standard only support 3 buttons per player, which might have sth to do with the problem, but not likely.
Test in NOTEPAD again. If you are using the default layout, you should get "i" for P2 B5, and "k" for P2B6.
If you're not using the default layout, make sure P2 B5 and P2 B6 aren't set to the same settings as one of the other keys.
If this checks out, start MAME start KI, hit TAB and inputs this game. Make sure the inputs match what you expect. Especially, make sure P1 --BINGO! Either that, or I was attempting to say "before" but it was too many letters to type--, 5 or 6 aren't set to something like "Z or I" or "I and k", etc.
If these are wrong, you can either fix it here, which overrides everything else, or create/fix controller.ini files to fix all the games.
If both of these are correct, then you need to look at wiring issues, or front end issues, but the steps above should troubleshoot most of it.