Which emu are you using for MAME/NeoGeo?
If you're using a libretro emu, you should be able to go into the RA menu (Hotkey+X by default), go to controls and there should be controls for User 1 Coin 1, User 2 Coin 2, etc.
Set them all to the same input, whichever input your coin controller is mapped to.
Do you have other buttons available on your USB joystick encoder? Maybe try setting it to another button instead of an axis?