First, Awesome work on ACF!
Just a Note: It looks like metaboxes aren’t honoring “Screen options” to turn on or off the metabox. While this works when the user clicks “Screen options” to hide a given metabox (jQuery toggles display:none/block), it’s not remembering the user set preferences.
I’ve tracked the line down for you at line #714 in everything_fields.php. It looks like there is no initial style=”display: …” set. This needs to pull the user’s set value or leverage WP’s hidden_meta_boxes filter to know what the initial value is/should be.
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