Index: wp-includes/default-filters.php
===================================================================
--- wp-includes/default-filters.php	(revision 18619)
+++ wp-includes/default-filters.php	(working copy)
@@ -255,6 +255,7 @@
 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/taxonomy.php
===================================================================
--- wp-includes/taxonomy.php	(revision 18619)
+++ wp-includes/taxonomy.php	(working copy)
@@ -2446,7 +2446,7 @@
 	} else {
 		// Default count updater
 		foreach ( (array) $terms as $term) {
-			$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships WHERE term_taxonomy_id = %d", $term) );
+			$count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->term_relationships INNER JOIN $wpdb->posts ON $wpdb->term_relationships.object_id = $wpdb->posts.ID WHERE $wpdb->term_relationships.term_taxonomy_id = %d AND $wpdb->posts.post_status != 'trash'", $term) );
 			do_action( 'edit_term_taxonomy', $term, $taxonomy );
 			$wpdb->update( $wpdb->term_taxonomy, compact( 'count' ), array( 'term_taxonomy_id' => $term ) );
 			do_action( 'edited_term_taxonomy', $term, $taxonomy );
Index: wp-includes/post.php
===================================================================
--- wp-includes/post.php	(revision 18619)
+++ wp-includes/post.php	(working copy)
@@ -2727,12 +2727,6 @@
 	$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);
@@ -5294,4 +5288,20 @@
 }
 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
+ * @since 3.3.0
+ */
+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 ) {
+		$tt_ids = wp_get_object_terms( $post->ID, $taxonomy, array( 'fields' => 'tt_ids' ) );
+		wp_update_term_count( $tt_ids, $taxonomy );
+	}
+}
 ?>