I’m also having issues with checkboxes that default to checked. My fields are implemented via PHP, so if 'default_value' => 1 then the field always appears checked on edit screens, and if the associated post is saved, the field is cleared/removed from postmeta (though I should note that the hidden _name meta remains).
Testing shows that defaulting the field to unchecked (i.e. 0) allows the field to display and store the data properly.
