fixes #356

lib/Doctrine/Query.php

@@ -699,7 +699,9 @@ class Doctrine_Query extends Doctrine_Query_Abstract implements Countable
 
         // parse the DQL parts
         foreach ($this->_dqlParts as $queryPartName => $queryParts) {
-            $this->parts[$queryPartName] = array();
+            
+            $this->removeQueryPart($queryPartName);
+
             if (is_array($queryParts) && ! empty($queryParts)) {
 
                 foreach ($queryParts as $queryPart) {
@@ -801,6 +803,7 @@ class Doctrine_Query extends Doctrine_Query_Abstract implements Countable
         $q .= ( ! empty($this->parts['orderby']))? ' ORDER BY ' . implode(', ', $this->parts['orderby'])  : '';
 
         if ($modifyLimit) {    
+
             $q = $this->_conn->modifyLimitQuery($q, $this->parts['limit'], $this->parts['offset']);
         }