The game throws "Skipping bad option" warnings for multiple settings, regardless of the values they're set to (even for correct values):
enableVsync
fullscreen
maxFps
forceUnicodeFont
This message is also shown incorrectly in other cases (i.e. setting the max framerate to Unlimited or getting an empty lastServer, see MC-141766 and MC-104818 respectively). But this is the only case where they appear regardless of how they're set up, and, in addition to that, show no signs of being "incorrect" in any manner. I've tested them with multiple values and the messages always seem to be shown.
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Uh? This and MC-141766 are not the same bug 😛
This has happened to me as well. It also happens with my controls, being set to the default every time.