diff --git a/lib/Doctrine/Query.php b/lib/Doctrine/Query.php
index 27d778016..43c54321e 100755
--- a/lib/Doctrine/Query.php
+++ b/lib/Doctrine/Query.php
@@ -1517,6 +1517,8 @@ public function getLimitSubquery()
 
         // add driver specific limit clause
         $subquery = $this->_conn->modifyLimitSubquery($table, $subquery, $this->_sqlParts['limit'], $this->_sqlParts['offset']);
+        // apply any outstanding indexes to the subquery before we rebuild the query parts using new Aliases
+        $subquery = $this->_applyIndexesToQuery($subquery);
 
         $parts = $this->_tokenizer->quoteExplode($subquery, ' ', "'", "'");
 
@@ -1586,6 +1588,7 @@ public function getLimitSubquery()
         }
 
         $subquery = implode(' ', $parts);
+
         return $subquery;
     }
 
@@ -2112,7 +2115,7 @@ public function getCountSqlQuery()
                 . $this->_conn->quoteIdentifier('dctrn_count_query');
         }
 
-        return $q;
+        return $this->_applyIndexesToQuery($q);
     }
 
     /**
diff --git a/lib/Doctrine/Query/Abstract.php b/lib/Doctrine/Query/Abstract.php
index a5ff0a10b..9b472b609 100755
--- a/lib/Doctrine/Query/Abstract.php
+++ b/lib/Doctrine/Query/Abstract.php
@@ -1059,8 +1059,6 @@ protected function _execute($params)
             $query = $this->_view->getSelectSql();
         }
 
-        $query = $this->_applyIndexesToQuery($query);
-
         // Get prepared SQL params for execution
         $params = $this->getInternalParams();
 
@@ -2503,8 +2501,7 @@ protected function _applyIndexesToQuery($sql)
                 }
             }
         }
-        // Empty the index part array to prevent us from accidentally appending twice.
-        $this->_index_parts = [];
+
         return $sql;
     }
 
diff --git a/lib/Doctrine/RawSql.php b/lib/Doctrine/RawSql.php
old mode 100644
new mode 100755
index 199fde9b8..10f844f3c
--- a/lib/Doctrine/RawSql.php
+++ b/lib/Doctrine/RawSql.php
@@ -283,7 +283,7 @@ public function getSqlQuery($params = array())
         if ( ! empty($string)) {
             array_pop($this->_sqlParts['where']);
         }
-        return $q;
+        return $this->_applyIndexesToQuery($q);
     }
 
 	/**
@@ -326,7 +326,7 @@ public function getCountSqlQuery($params = array())
             array_pop($this->_sqlParts['where']);
         }
 
-        return $q;
+        return $this->_applyIndexesToQuery($q);
     }
 
 	/**