Index: wp-includes/default-filters.php
===================================================================
--- wp-includes/default-filters.php	(revision 18579)
+++ wp-includes/default-filters.php	(working copy)
@@ -252,6 +252,7 @@
 add_action( 'publish_post',               '_publish_post_hook',       5, 1 );
 add_action( 'save_post',                  '_save_post_hook',          5, 2 );
 add_action( 'transition_post_status',     '_transition_post_status',  5, 3 );
+add_action( 'transition_post_status',     '_update_term_count_on_transition_post_status',  10, 3 );
 add_action( 'comment_form', 'wp_comment_form_unfiltered_html_nonce'        );
 add_action( 'wp_scheduled_delete',        'wp_scheduled_delete'            );
 add_action( 'admin_init',                 'send_frame_options_header', 10, 0 );
Index: wp-includes/post.php
===================================================================
--- wp-includes/post.php	(revision 18579)
+++ wp-includes/post.php	(working copy)
@@ -2726,12 +2726,6 @@
 	$post->post_status = 'publish';
 	wp_transition_post_status('publish', $old_status, $post);
 
-	// Update counts for the post's terms.
-	foreach ( (array) get_object_taxonomies('post') as $taxonomy ) {
-		$tt_ids = wp_get_object_terms($post_id, $taxonomy, array('fields' => 'tt_ids'));
-		wp_update_term_count($tt_ids, $taxonomy);
-	}
-
 	do_action('edit_post', $post_id, $post);
 	do_action('save_post', $post_id, $post);
 	do_action('wp_insert_post', $post_id, $post);
@@ -5293,4 +5287,24 @@
 }
 add_filter( 'wp_get_object_terms', '_post_format_wp_get_object_terms' );
 
+/**
+ * Update the custom taxonomies' term counts when a post's status is changed. For example, default posts term counts (for custom taxonomies) don't include private / draft posts.
+ * 
+ * @access private
+ * @param string $new_status
+ * @param string $old_status
+ * @param object $post
+ */
+function _update_term_count_on_transition_post_status( $new_status, $old_status, $post ) {
+
+	// Update counts for the post's terms.
+	foreach ( (array) get_object_taxonomies( $post->post_type ) as $taxonomy ) {
+		if( empty( get_taxonomy( $taxonomy )->update_count_callback ) )
+			continue;
+	
+		$tt_ids = wp_get_object_terms( $post->ID, $taxonomy, array( 'fields' => 'tt_ids ') );
+		wp_update_term_count( $tt_ids, $taxonomy );
+	}
+
+}
 ?>