I am talking into the void at this point on this thread but I did find a solution for this for anyone searching the interweb in the future like I was. I end arounded this "joystick 1" problem with hardware. I purchased an additional USB controller board ($10) and configured it as well. Once I determined which board advmame assigned to J1 I just moved the joystick wiring to the other board that was assigned J3 then remapped in the Tab menu to those controls. I now technically have 3 controllers but only 2 actual functional controllers on the arcade control panel itself. I would guess there is a software way to fix this but it was way easier to eat $10 and save the time and hassle of troubleshooting and hours of reading config files with no actual knowledge :)