This issue is a serious annoyance. I use the PS4 controller with no ppjoy or x360ce or anything (I was initially using x360ce and I thought that was the problem, but I got rid of it and it still happens, and it seems it's happening to a bunch of people with and without input wrappers). Like people who posted before, I only use my controller for this game, and only for flying planes, so most of the time the controller is not plugged in (I take it back to the other room to play on the ps4). Having to redo all my settings, even the ones not related to controller input, every time I start the game after having used the controller is pretty annoying.