EntityFieldQuery breaks for non-node entities

I have the following query ($entity_type is not a node):

$query = new EntityFieldQuery();
$query->entityCondition('entity_type', $entity_type)
         ->entityCondition('bundle', $bundle)
         ->propertyCondition('uid', $uid)
         ->propertyCondition('status', 1)
         ->fieldCondition('field_some_field', 'value', '1', '=');

This worked ok before I had to install this module and rebuild permissions.
After I did that, the query is altered and the following part added:

AND ( EXISTS (SELECT na.nid AS nid FROM {node_access} na WHERE (( (na.gid = :db_condition_placeholder_6) AND (na.realm = :db_condition_placeholder_7) ))AND (na.grant_view >= :db_condition_placeholder_8) AND (field_data_field_some_field0.entity_id = na.nid) )) AND(( (field_data_field_some_field0.entity_type = :db_condition_placeholder_9) )OR (field_data_field_some_field0.entity_type <> :db_condition_placeholder_10) )

After I disabled this module, everything went back to normal.