Index: wp-includes/taxonomy.php
===================================================================
--- wp-includes/taxonomy.php	(revision 12135)
+++ wp-includes/taxonomy.php	(working copy)
@@ -180,13 +180,13 @@
 		$wp->add_query_var($args['query_var']);
 	}
 
-	if ( false !== $args['rewrite'] && !empty($wp_rewrite) ) {
+	if ( false !== $args['rewrite'] && '' != get_option('permalink_structure') ) {
 		if ( !is_array($args['rewrite']) )
 			$args['rewrite'] = array();
 		if ( !isset($args['rewrite']['slug']) )
 			$args['rewrite']['slug'] = sanitize_title_with_dashes($taxonomy);
 		$wp_rewrite->add_rewrite_tag("%$taxonomy%", '([^/]+)', $args['query_var'] ? "{$args['query_var']}=" : "taxonomy=$taxonomy&term=$term");
-		$wp_rewrite->add_permastruct($taxonomy, "{$args['rewrite']['slug']}/%$taxonomy%");
+		$wp_rewrite->add_permastruct($taxonomy, "/{$args['rewrite']['slug']}/%$taxonomy%");
 	}
 
 	$args['name'] = $taxonomy;
@@ -2213,7 +2213,7 @@
 	$slug = $term->slug;
 
 	if ( empty($termlink) ) {
-		$file = get_option('home') . '/';
+		$file = trailingslashit(get_option( 'home' ));
 		$t = get_taxonomy($taxonomy);
 		if ( $t->query_var )
 			$termlink = "$file?$t->query_var=$slug";
Index: wp-includes/category-template.php
===================================================================
--- wp-includes/category-template.php	(revision 12135)
+++ wp-includes/category-template.php	(working copy)
@@ -768,7 +768,7 @@
 	$slug = $tag->slug;
 
 	if ( empty( $taglink ) ) {
-		$file = get_option( 'home' ) . '/';
+		$file = trailingslashit(get_option( 'home' ));
 		$taglink = $file . '?tag=' . $slug;
 	} else {
 		$taglink = str_replace( '%tag%', $slug, $taglink );