Heh, no problem.. That makes things a little more clear. But still, if everything works in the control panel, and it works in some games, then I can only assume that MAME is set up to properly recognize the control. At this point, you need to make sure that the games you play are set up to recognize the way you have the board wired. If you already have custom configurations set up, the default configuration will be ignored. You may have to delete, or edit the custom configs to reflect the current control scheme.
RandyT