Added copy() method to Query.php and made NestedSet.php use it because native clone() does not work. Also Added ->getSql() to getRootAlias() so that _aliasMap is present after the parsing.

lib/Doctrine/Hydrate.php

@@ -179,6 +179,8 @@ class Doctrine_Hydrate extends Doctrine_Object implements Serializable
      */
     public function getRootAlias()
     {
+        $this->getSql();
+        
         reset($this->_aliasMap);
 
         return key($this->_aliasMap);

lib/Doctrine/Query.php

@@ -1531,4 +1531,17 @@ class Doctrine_Query extends Doctrine_Query_Abstract implements Countable
 
         return $this->execute($params);
     }
-}
+    
+    public function copy(Doctrine_Query $query = null)
+    {
+        if( !$query )
+        {
+          $query = $this;
+        }
+        
+        $new = new Doctrine_Query();
+        $new->_dqlParts = $query->_dqlParts;
+      
+        return $new;
+    }
+}

lib/Doctrine/Tree/NestedSet.php

@@ -269,7 +269,7 @@ class Doctrine_Tree_NestedSet extends Doctrine_Tree implements Doctrine_Tree_Int
         if (!isset($this->_baseQuery)) {
             $this->_baseQuery = $this->_createBaseQuery();
         }
-        return clone $this->_baseQuery;
+        return $this->_baseQuery->copy();
     }
     
     /**