Plugin Options Not Saving to Database in WP 4.5

This is probably the root cause – https://core.trac.wordpress.org/changeset/36510. Core have moved from saving menus in $_POST to sending them as json encoded and then decode it into $_POST. I am not very familiar with how menus are sent to the server, but you probably either use the wrong hook, use the right hook but too early, or there is a bug in core.

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