If I go to (for example), meta, and create a global override, and disable the VE beta feature, its not actually disabled, and when I look at my preferences again, it shows that the beta feature is still enabled. This also happens with some other preferences, like the compact language list on enwiki.
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The only thing in the console when I test it on meta is JQMIGRATE: Migrate is installed with logging active, version 3.0.1, which I'm pretty sure isn't related to this.
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(marking as resolved rather than invalid because I think the issue went away, rather than there not being an issue to begin with)