Index: wp-includes/taxonomy.php
===================================================================
--- wp-includes/taxonomy.php	(revision 16914)
+++ wp-includes/taxonomy.php	(working copy)
@@ -329,7 +329,7 @@
 			$tag = '([^/]+)';
 
 		$wp_rewrite->add_rewrite_tag("%$taxonomy%", $tag, $args['query_var'] ? "{$args['query_var']}=" : "taxonomy=$taxonomy&term=");
-		$wp_rewrite->add_permastruct($taxonomy, "{$args['rewrite']['slug']}/%$taxonomy%", $args['rewrite']['with_front']);
+		$wp_rewrite->add_permastruct($taxonomy, "{$wp_rewrite->root}{$args['rewrite']['slug']}/%$taxonomy%", $args['rewrite']['with_front']);
 	}
 
 	if ( is_null($args['show_ui']) )