I am using featured video plus to offer our client to add video's to custom post types. In our last release I changed the public property of the custom post types to false. The reason I did this was because we don't want to have rewrite rules for them or have them in the search and public manages this very quickly and cleanly. I then put show_ui on true so the client could still edit the custom post type.
This had the negative side effect that the featured video plus setting wasn't displayed anymore, I searched in the plugin's code and found the location where it went wrong.
On line 89 of the file php/backend.php there is the following line:
$post_types = get_post_types(array("public" => true));
This means our post types don't get a custom meta box. Could you change this to:
$post_types = get_post_types(array("show_ui" => true));
Because that is more accurate to what you want to achieve.