That should configure input for RetroArch universally. Can you control the RetroArch menu ui with your gamepad or is it only that one core?
Like dugan suggested can you tell us what input driver you are using with RetroArch? You can tell by looking in 'settings -> driver' or with this command.
Code:
grep input_driver ~/.config/retroarch/retroarch.cfg
If you are using the 'udev' input driver I would suggest you either use the 'x' input driver instead or be sure to read README.SLACKWARE included with the slackbuild and then make sure your user is part of the input group.
Edit: If problems persist, the output of 'retroarch --verbose' when your gamepad is plugged in could help.