I'm not sure if it's entirely correct, but... I do know the game only saves the UI settings at certain points, not every time they change. And there are infamously several ways to leave a character that don't cause the UI settings to be saved (eg. /exit vs. proper camping out). So when I see minor weirdness (most common is the group or raid window open on camp-in, followed for me by the character window being up) I figure it can't hurt to clean up and force the settings to be saved and usually I don't have it happen again for a good long while.
What's more annoying is joining a group or raid and not having the group or raid window auto-open. But that seems to be a game-client issue, possibly it thinks I've closed those windows manually so it doesn't automatically change their state.
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