@grale22 And remember that Arcade is a folder, not an emulator so it's important to know which emulator you are dealing with. See here:
https://github.com/retropie/retropie-setup/wiki/MAME#arcade

Just a quick update on the situation.
As barbudreadmon recommended I updated my romset for the games that would run only with the pifba emulator and now I can play them with the lr-fbalpha emulator! Which again doesn't need any further controller settings since I had everything done already.
It did not solve my issue with the pifba but updating the romset made it unnecessary to fix.

Thanks again for the quick help. I think I'll go grab a beer and start playing.
Cheers.

@markyh444

Roger that. Will do. Thx.

@hansolo77 Thanks.

You may have a file named /opt/retropie/configs/all/retroarch-joypads/MayflashLtdMayflashMDUSBAdapter.cfg or something. AFAIK, RetroArch will get the configs from this file no matter if you have a MegaDrive or an Atari 2600 controller plugged. It can be annoying.

When you want to come back to this issue, my suggestion is to hardcode the mappings for atari2600 in the file /opt/retropie/configs/atari2600/retroarch.cfg (you may want to have a keyboard plugged in order to solve the issues you mentioned for start button, etc.). You can get the instructions on how to edit it on the wiki: https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration#hardcoded-configurations

Thanks. The problem then is bad wiring or a fault as they normally map to different keys.

I posted the working configs in my process thread here:
https://retropie.org.uk/forum/post/46824

But honestly, you'll benefit from doing the work yourself too. One of the things in particular is that the controller I'm using (Wireless Xbox360) is mapped on my device as Joystick #5, and Event #7. If you only have 1 controller, yours may be listed as something like Joystick #0 and Event #1 or something. Also, it looks like it's picking up a serial number or something in the actual device name, so it might not work at all. But you're more than welcome to give it a try, maybe you'll get lucky. Also, I'm using the default keyboard mapping in the game, so if you've changed it, you'll want to reset it.

I just double checked, and it doesn't look like the the port assignment is needed for anything more than identifying the actual button maps. The configuration uses by-id so it'll work no matter what port or joystick # it's assigned to. The only issues you'd have would be if the controller you're using ISN'T the same, and if the ID is incorporating a serial number.

Thanks. I googled how to do that and it worked :).

@pirossi haha. Good metaphor! ;-)

Reviving this, because I just found out that you can have the hotkey act as a dedicated pausekey if in Retroarch you assign it to the same button press.

In my situation, my middle front button on my arcade is mapped to keyboard "o".
In Retroarch I assigned both my hotkey and my toggle pause key to "o", and this means that games pauses when I press it, but it still serves as a hotkey, so the other hotkey commands works as well (though the game pauses).

Not sure if this will work as an exit button (the game will then exit when you hotkey), but with pause it does!

wow. I can't believe I didn't reconfigure the joypad in ES afterwards. What an obvious thing to try. I just assumed I was modding the .cfg from the menu. All is working now. Thanks for the assistance!

@vbs you're right. And it was already fixed. :-)
Cheers!

@BuZz ok, thank you

@klay824 Glad to know that you managed to fix it, albeit in this radical way. I gave up and jumped to Recalbox for the time being, I found it to be more user friendly to someone as useless as I am in Linux.

@aaaccc1

Remapping the core controls will not affect the the main control configs at all. Rather, it will create a new .rmp file that will be automatically loaded everytime the core is loaded. Should you ever decide to switch back, you could just return the core remapping to it's original state by changing the controls back and saving the core remapping again, or if you don't happen to remember what they, you can always just delete the remapping file altogether. At that point, RetroArch would have no remapping file to load, leaving the original control scheme in tact.