Hi! I just started using retropie now (the V3.0 beta 4), and I’m having kinda the same problem. I’m using a generic controller, and can’t save the config of the analogics.
I’ll leave the topic that me and another users where trying to find a solution, as reference:
http://blog.petrockblock.com/forums/topic/dualshock-4-snes-problems/
Falcon found a solution for his dualshock 4, but he is using it for playing snes and gba. So, I dunno if his analogs have the same problem as mine:
I also am using a Dualshock 4 (PS4) controller, and had the same issue, but I finally found out a solution!
After looking through some of the setup options, one of the options was Install Retroarch autoconfigs (or something like that, it was very similar). I decided to just give it a whirl and install this, and it ended up working! I rebooted my Pi, went into Super Mario World for SNES and it worked perfectly.
Also tested on The Legend of Zelda Minish Cap for GBA. Works fine! I hope this helps!
I did not have to go back in and configure the controller manually after this. I just rebooted my Pi and it was already configured correctly.