I don't use a controller on PC for ages, but I remember back in the day this was an issue that plagued me a lot, especially the keybindings messing up if I quickly change from controller to M&K in Galactic Assault.
Another thing which happens to me to this day is the issue with the controller turning off. Even if I reconnect it, the game needs to be restarted for it to be recognized again. I don't use a controller to play anymore, as I stated before, but I do use to test stuff in Arcade Splitscreen. However as it's a mod, and my controller is a PS3 controller, which needs a special software to be recognized by windows, I never bothered reporting about it. But I feel it may be connected to the issue people have been reporting here.
