I`ve got stuck with this problem too, posts which post types were not public are saved with post type post, instead of the correct custom type.
In order to make it work with Advanced Custom Fields and (maybe) other plugins, just add these lines to the function save_post, in post-type-switcher.php under /wp-content/plugins/post-type-switcher:
...function save_post( $post_id, $post ) {
//changed in order to do not change hidden custom post-types
if( get_post_type_object($post->post_type)->public == false)
return;
...
