Users are getting unsubscribed from lists no matter what.

This will fix it in emf_user():

// unsubscribe from all known lists
if (variable_get('emf_account_status_sync', 0)) {
  $lists = emf_db_get_lists();
  foreach ($lists as $list) {
    emf_db_save_request('unsubscribe', $mail, $list->lid);
  }
}