errors when configuring module, or saving nodes

This should be fixed in latest 7.x-2.x-dev.
You should try to update the code, then clear the site caches, and re-submit the "field settings" form.

I don't think I see what code change in References might cause this.

- Do you know what was the previous code version you had ? beta3 ? some other state of -dev ? (any idea of the date ?)
- Did you upgrade other modules (or drupal core) at the same time ?

Trying to understand what is happening on your setup.

- The changes from beta-3 to current -dev have no reason to cause the messages you mentioned in #2. Those are caused by the fact that the $field definition that lies in your 'field_config' db table has no 'indexes' entry (it should be in the serialized 'data' column).
I'm not sure why that is, and that would deserve investigation, but that is something that is controlled by core, and upgrading the References code did not provoke that. I'd think that submitting the "field settings" form would have caused this error even before you upgraded References.

Please enable devel.module if you haven't, go to devel/php, execute the code below (I guessed the field name from the errors you posted), and post the result here (preferably uploaded in a .txt file)

$field = field_read_field('field_service_maintatiner');
dsm(var_export($field, TRUE));

- Those errors you mention in #2 do not relate to "make the effected field unviewable", so I'd need you to be more specific on that part. What goes wrong when you do what and where ? Are there any error messages ?

I'm not familiar with node_access_user_reference.module, but from a quick look at the code I don't see where it would interfere.

I don't see what's wrong with the ids in the dumps you posted above.
"Redid it and got a different ID?" - I don't understand what you mean. As you can see I'm trying to help you debug your site, but if you don't make the effort to be clearer I can't do much to help.

My only suggestion right now is to run the following code in devel/php to fix the missing 'indexes' entries in the field_config table.
Please backup your database beforehands.

$records = db_query('SELECT * FROM {field_config} WHERE deleted = 0')->fetchAll();
foreach ($records as $record) {
  $data = unserialize($record->data);
  if (!array_key_exists('indexes', $data)) {
    dsm('Fixing missing indexes info in ' . $row->field_name);
    $field = field_read_field($record->field_name, array('include_inactive' => TRUE));
    module_load_install($record->module);
    $schema = (array) module_invoke($record->module, 'field_schema', $field);
    $data['indexes'] = isset($schema['indexes']) ? $schema['indexes'] : array();
    dsm($data['indexes'], $record->field_name);
    db_update('field_config')
      ->fields(array('data' => serialize($data)))
      ->condition('field_name', $record->field_name)
      ->execute();
  }
}
drupal_flush_all_caches();

OK, cool :-)
I'll push a new release with the recent changes ASAP.

typo