I have a couple of Logitech 310 USB controllers. Using one or both, every time I load a ROM in RetroPie 3.5 OR 3.6, I have to unplug and replug the controllers for them to be seen by the emulator.
I have tried multiple pi’s, clean installs of everything, and it keeps happening. Everything works fine in the ES menus regardless, but once opening the emulators, I have to unplug (seeing the disconnect message) and replug (seeing the reconnect message).
Some times Retroarch keeps on seeing the wrong controller as the default one (no mater what you set in the setup shell script). I too have to disconnect one of my controllers for a certain controller to work in games that use Retroarch for its config.