Well, ordinarily you'd just do whatever you did to configure the other controls: Go into the in-game configuration menu using the TAB key, select Player 1, then select the function you want mapped to that button and press the button to register it. The key is to not release the button right away as it can take several seconds to register with the program.
You may have already done this to get the buttons working that do so presently, so if you know how to do this and it's just not working, then I'd suggest disconnecting and reconnecting the entire controller setup and replugging the joypad into the adapter and trying that. I've had issues with my Lik-Sang Boom 64 adapter occasionally not making a good connection with the controller, so it's not impossible. Otherwise more knowledgeable people than myself will know how to troubleshoot controller issues; in fact there may already be threads concerning this, so do a search, but I cannot say that I've seen a controller only work partially before.