Hi.

In taxonomy.module, there is an implementation of hook_options_list()

/**
* Implements hook_options_list().
*/
function taxonomy_options_list($field, $instance, $entity_type, $entity) {
  $function = !empty($field['settings']['options_list_callback']) ? $field['settings']['options_list_callback'] : 'taxonomy_allowed_values';
  return $function($field);
}

As you seen, it works perfectly with custom options_list_callback in taxonomy_term_reference. But with your modules, I cannot do like that. Could you please change your hook_options_list() to these one? Thank you

/**
* Implements hook_options_list().
*/
function node_reference_options_list($field) {
  $function = !empty($field['settings']['options_list_callback']) ? $field['settings']['options_list_callback'] : '_node_reference_options';
  return $function($field, FALSE);
}

/**
* Implements hook_options_list().
*/
function user_reference_options_list($field) {
  $function = !empty($field['settings']['options_list_callback']) ? $field['settings']['options_list_callback'] : '_user_reference_options';
  return $function($field, FALSE);
}