Im having the same problem this is how it happens:
Using DragonRise Inc. Generic USB Joystick
autoconf file: https://pastebin.com/uRzdUd2C
1 - Open Retroarch.
2 - Controler autoconf message pops up in the bottom of the screen. At this point everything is working great.
3 - Load a game from any core, the game works normally. but the autoconf message does not pop in the bottom of the screen. So the controller does not work.
4 - So now i have to unplug the controller and plug it back in. After plugging the controller back in, the autoconf message pops up at the bottom of the screen. and the controller works again.
It happens all the time, when changing shadders, when exiting a game, while opening a game.
So I have to keep unplugging and plugging the controller back in for the autoconf message to appear at the bottom of the screen.
I have no problem when using a Logitech f310.
Sorry for my bad english.