I've been able to reproduce this changing any key input. From what I see something similar to companion behavior is happening and controls reset to the last selected control mode aside from custom changing the custom controls to the same keybinds every launch.
Edit: If last selected was Mystery before Custom, Mystery will be selected on relaunch and change custom keybinds
If VI was last selected before Custom, VI will be selected on relaunch and change custom keybinds, etc
It's also worth noting that keys can share a keybind currently