@Marconemusic If I understand you correctly, everything works except Mame Controls are not mapped how you want, is that correct? If this is true, it sounds like you have to remap your controls for mame emulator. I have an arcade cabinet and when I mapped my controls, I mapped my joystick as D-Pad. I have no analog stick mapped with my joysticks. If I use an Xbox One Controller, I map everything accordingly but outside of that, I don't have an analog stick mapped.
Even when I did use my Xbox One controller, Mame and Final Burn did not recognize my analog stick. If Mame is the only thing mapped incorrectly, try remapping your controls for Mame. You can hit tab on your keyboard within Mame and you can set your controller mapping there for the General mapping or for each game.
If your Emulation Station also isn't mapped correctly, you may have to remap the controls for that input device. One time I had issues when I was building mine and controllers got reversed between player one and 2 when I didn't plug my inputs into the same USB port they were before. When I plugged in them in how I had it, it fixed that issue.
