I can think of two possibilities. First is to make sure your reset the input mapping (since you didn't meanition on how you reset the settings). The quickest way is to delete the cfg folder, but you can also just delete the default.cfg file in that folder. (You might want to back it up first if you remapped anything intentionally.)
If that doesn't help, your two buttons' wiring might be lose, and doesn't stay down long enough for mame to see. If you hold either of them down in notepad, does it act like the other, working, buttons?