I remember having issues with both input methods attached and being switched a long time ago. Nowadays I only use controller for testing purposes on the splitscreen mod for PC, so I don't actually change from one another, player 1 is M&K and player 2 is Controller.
But back when I used to play Starships, I used a controller. In GA I would switch from Controller to M&K and vice-versa whenever I changed from Ground to Starship, and then back to Ground. Sometimes my character would get stuck looking downwards, and my Mouse buttons assignment would change. If I got back to the controller it would also behave erratically. I used to fix this by just removing the controller and stop playing as a Starfighter (no wonder why I never played Starfighters anymore), but that fixed the issue for M&K, not for the controller.
I hope devs decide to improve this situation, but as seeing it's a PC only issue, I don't think this will ever get prioritized.
