Beta 4 - Game doesn't save fullscreen setting when changed with keyboard command

[SoItBegins]

This one's simple to describe. If you change the game's fullscreen setting in the Options window, it will be saved (so if you set the game to windowed, the app'll open windowed next time it starts). However, if you use the keyboard shortcut, your new fullscreen/windowed setting won't be saved (so if you start in fullscreen, then use the shortcut to switch to windowed, the game will start in fullscreen next time you run it.)
Is this on purpose?