It will only take effect when you hit play or restart the game, my bad design I guess, sorry. BTW, I guess you're using Linux, what distro is it (just curious)?
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I'm using Arch with i3 for windowing, which means it's using X11 and scales the applications directly after they are opened if it can (due to i3 being a tiling window manager).
Also, it's all good! It *is* a game jam entry, and if bugs like these weren't something to be expected; and this one really isn't game breaking either.