I use 2 controllers regularly. One is a DS4 and the other is a a 8bitdo Arcade Stick. Until recently Retroarch had no problems in recognizing the right controller and assigning the default profiles.
Some weeks ago, I played Sunset Riders (FB Neo), and had to disable port 1 controls and assign the arcade stick to port 3 so I could play with the 3rd characters.
Ever since then, Retroarch never worked again properly. The DS4 only works through DS4 windows, and retroarch recognizes 2 controllers “wireless controller” and “xbox 360 controller”, this was never a problem before, because it would always assign the “xbox controller” to port 1. Not it does assign the “wireless” controller, which doesn’t work, and I have to change the controller and remap every time I want to play (loading the controller profile just doesn’t work). If I turn off DS4 windows, it just recognizes the “wireless controller”, and it just doesn’t work.
And ever since I did that thing with Sunset Riders, If I start retroarch with the arcade stick, it gets detected, but the player 1 port is disabled. I have to enable it every single time, and remap the controls. I load the controller profile, but it also doesn’t change anything.
I have in the settings the autoconfig/plug and play on.