Retroarch, Blissbox, and controller mapping

[TheNewClassics]

Hey Launchbox community.

So I've got a bit of a conundrum I'd like to present, and see if someone can help me out. I have a Blissbox 4-Play, and use Retroarch for a good portion of my systems; for this example we'll use Genesis and Sega Saturn. I have a Blissbox 4-Play with original controllers for both systems. Now, I plug in a Genesis controller, and load up a Genesis game. Retroarch is currently set to autoconfig enable. I get a message saying something along the lines of "4-Play GEN 6 configured in Port #0". I go into input mapping in Retroarch, and the inputs for the core (Genesis Plus GX) are what I would want for the Genesis controller. I exit the game back to BigBox. Now I can unplug the Genesis controller, plug in a Saturn controller, and load up a Saturn game using the mednafen_saturn core of retroarch. The input mapping is wrong, and I need to change it, even though Retroarch says "4-Play Saturn Digital configured in Port #0). I fix the inputs and exit.

Now the cycle seems to repeat itself. I can load up Genesis through Retroarch, and the inputs are wrong again. What I cannot figure out is what the problem is; is it because I have autoconfig enabled? Is it because I need to change a setting in Retroarch to enable per-core input mapping? This one has stumped me, and I'm beginning to wonder if it's because of autoconfig. However the autoconfig files in my Retroarch folder seem to have the appropriate inputs for each specific controller, so I can't explain that.

If anyone has any thoughts, I'd appreciate it. In an ideal world I'd like to be able to just switch controllers when I want to play a different system, load up the game and have the right inputs each time. I thought autoconfig would do that but I could be wrong.

Of note, I used Rocketlauncher for years, and I believe it had an option for per-core settings; I would essentially just use this for each system and bypass this problem. However I wasn't using autoconfig at that time, and I was hoping that this option might make life easier if I could figure out how to use it correctly. 

Edited July 10, 2018 by TheNewClassics