I haven't tried it using FBneo so maybe I'll do that. Failing that I'll just get hold of the NES version I guess.

@seannyboy08 Can't know without finding the cause of the issue.

@mitu thank you! So once I do this, it will allow me to choose if I use the joystick/controller for a game? Do I have to input the user binds for each input?

@iandaemon one option might be to use one of these atari flashback joysticks. Haven't tested myself but it supports the extra buttons youd need
https://www.ebay.com/i/224271746915?chn=ps&norover=1&mkevt=1&mkrid=711-117182-37290-0&mkcid=2&itemid=224271746915&targetid=1071875433821&device=m&mktype=pla&googleloc=9006120&poi=&campaignid=11615400122&mkgroupid=112424567959&rlsatarget=pla-1071875433821&abcId=9300455&merchantid=113614495&gclid=Cj0KCQiAw_H-BRD-ARIsALQE_2NAYW9crkX2MnAaNxYeq363HaNKnmi_Taqe8okU9BhZLu5xfbP-rccaAufPEALw_wcB

It was that indeed. Sorry, I had forgotten that I had a previous emulationstation (yes, from Ubuntu repos) install in the machine. I just re-installed the machine, and got everything from the RetroPie-Setup script this time. It works like a charm!

Thanks a lot for you help!

@r3fear that screen is started by Emulationstation, so you cannot use a script to launch it, since it's within the application itself.