Index: wp-includes/version.php
===================================================================
--- wp-includes/version.php	(revision 8615)
+++ wp-includes/version.php	(working copy)
@@ -15,6 +15,6 @@
  *
  * @global int $wp_db_version
  */
-$wp_db_version = 8585;
+$wp_db_version = 8586;
 
 ?>
Index: wp-includes/rewrite.php
===================================================================
--- wp-includes/rewrite.php	(revision 8615)
+++ wp-includes/rewrite.php	(working copy)
@@ -447,8 +447,9 @@
 		}
 
 		if (empty($this->category_base))
-			$this->category_base = 'category';
-		$this->category_structure = trailingslashit( $this->front . $this->category_base );
+			$this->category_structure = trailingslashit( $this->front . 'category' );
+		else
+			$this->category_structure = trailingslashit( '/' . $this->root . $this->category_base );
 
 		$this->category_structure .= '%category%';
 
@@ -466,8 +467,9 @@
 		}
 
 		if (empty($this->tag_base))
-			$this->tag_base = 'tag';
-		$this->tag_structure = trailingslashit( $this->front . $this->tag_base );
+			$this->tag_structure = trailingslashit( $this->front . 'tag' );
+		else
+			$this->tag_structure = trailingslashit( '/' . $this->root . $this->tag_base );
 
 		$this->tag_structure .= '%tag%';