Index: taxonomy.install
===================================================================
--- taxonomy.install	(revision 3365)
+++ taxonomy.install	(working copy)
@@ -200,6 +200,7 @@
         'default'=> 0,
       ),
     ),
+    'primary key' => array('nid', 'tid'),
     'indexes' => array(
       'term_node' => array('tid', 'sticky', 'created'),
       'nid' => array('nid'),
@@ -816,3 +817,9 @@
   ));
 }

+/**
+ * Add a primary key to the {taxonomy_index} table
+ */
+function taxonomy_update_7011() {
+  db_add_primary_key('taxonomy_index', array('nid', 'tid'));
+}
\ No newline at end of file