Works for me, sorry I can't debug it on another site via comment/post communication.

To exclude customer notes and private notes generated by 'system', lines 39 - 46 become:
      foreach( $notes as $note ) {
        if( ! $note->customer_note ) {
          if( $note->added_by != 'system' ) {
            print '<li class="order_private_note">';
            $date = date( 'd/m/y H:i', strtotime( $note->date_created ) );
            print $date.' by '.$note->added_by.'<br>'.$note->content.'</li>';
          }
        }
      }