It was OK to deal with for a bit, but constantly reloading my keybinds is just getting old.
The issue is only happening in space. My keymaps for my mouse buttons keep resetting after each loading screen. I've specifically remapped how the ship drives with the mouse. Instead of holding both buttons down, I can hold the right mouse button only and it shifts the position of the camera to follow. I have Rbutton set to +CamTurnToFace and both Right and left drag set to +CamMouseLook.
Any idea why they are resetting after each load? I have not noticed if there have been other changes in the keymap, but from what I can see, the keyboard goes unchanged.