I've got my MiSTer setup with a JammASD which is connected to my Jamma harness. The same Jamma harness, when connected to my Jamma board (412 vertical games) works perfectly and all buttons respond in the input test.
However when connected to my MiSTer I can't get button 6 to respond at all.
Couple of questions:
Are there any troubleshooting steps I can take with this?
Usually there's not enough "free pins" in the JAMMA harness to have 6 buttons, the maximum amount you can wire normally is 5, as the MVS Neo Geo, which has pin 25 as D button and pin 26 as select. Pins 27 and 28 are both ground in the JAMMA standard. Usually any extra button beyond that needs to be wired directly in the board your are using (like the kick harness), althoug I know there's some JAMMA adapteres for Mister and other setups, where button 6 can be pin 27, but you would need to wire your JAMMA harness according to that.