Index: wp-includes/canonical.php
===================================================================
--- wp-includes/canonical.php	(revision 17521)
+++ wp-includes/canonical.php	(working copy)
@@ -164,8 +164,14 @@
 							$redirect['query'] = remove_query_arg( array( 'term', 'taxonomy'), $redirect['query']);
 					}
 				}
+
+				$tax_obj = get_taxonomy( $obj->taxonomy );
+				$tax_query_vars = array_diff( array_keys( $wp_query->query ), array_keys( $_GET ), array( 'taxonomy', 'term', $tax_obj->query_var ) );
+
 				$tax_url = parse_url($tax_url);
-				if ( ! empty($tax_url['query']) ) { // Custom taxonomies may only be accessable via ?taxonomy=..&term=..
+				if ( ! empty($tax_query_vars) ) {
+					//The request was for a custom permalink, so we have nothing to add here.
+				} elseif ( ! empty($tax_url['query']) ) { // Custom taxonomies may only be accessable via ?taxonomy=..&term=..
 					parse_str($tax_url['query'], $query_vars);
 					$redirect['query'] = add_query_arg($query_vars, $redirect['query']);
 				} else { // Taxonomy is accessable via a "pretty-URL"