Node reference and User reference

> Node reference and User reference fields

Do you mean those from http://drupal.org/project/references?

Both the project page and the code state that those aren't supported:

/**
 * Define the list of field types we work with.
 */
function reference_options_limit_get_field_types() {
  return array(
    'taxonomy_term_reference',
    'entityreference',
  );
}

Also, given that http://drupal.org/project/references states it will be soon deprecated, it's not something I'll be adding support for.

So yes, I suggest replacing your fields. Alternatively, I'll consider a patch for supporting these.