I also get this same issue. Every time I unplug my stick and shelf it until I play next I have to reconfigure everything. Often I have been launching DCS in hopes to play, then find out the controls have been reset, so I opt to load up my saved configs and cannot from within the game. I have to quit out to the DCSWorld launcher and load em up in the options there. Only then to return to the game with some controls mapped again.