Hi there,
i've noticed the same problem today. I've updated from version 4.0.0 to 4.0.2 but that wasn't the problem.
I also tried to configure the SNES-Emulator for using more than 2 controllers, for this i open the "Retroarch" inside of a game and just actitvated the option "Save Configuration On Exit" under Settings -> Configuration. Just after this step the problem with the Black Screen appears in every Emulator (SNES, N64, PS1...).
I've found the solution with the "Transition Style" here, and it worked for me, but i was interested why does this problem appears.
So i just started a SNES Game again and open the "RetroArch" menu again and just loaded the default settings from "etc/retroarch.cfg". I quit the game without the "BlackScreen"-problem. After that i switched back to "Slide" instead of "Fade" and noticed that the BlackScreen isn't appear anymore after i exit a game.
Hope this helps!
Greeting
Dolo