I have noticed that in the latest version (playing on Windows), some settings are not stored after quitting the game (or they are set back after the new start, I don’t know at which point it happens).
For example, the Smoothing and Filtering are reset each time (in the Controls section), same with the Camera distance (in the Graphics section). I don’t know if there’s anything else, these are just the settings I happened to notice. They seem to be working for an active session (i.e. they are saved properly while the game is running), but after the restart, they are always returning to their default values.