Index: wp-includes/comment.php
===================================================================
--- wp-includes/comment.php	(revision 37058)
+++ wp-includes/comment.php	(working copy)
@@ -2151,7 +2151,23 @@
 	$new = apply_filters( 'pre_wp_update_comment_count_now', null, $old, $post_id );
 
 	if ( is_null( $new ) ) {
-		$new = (int) $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->comments WHERE comment_post_ID = %d AND comment_approved = '1'", $post_id ) );
+
+		$bad_parents = array();
+		$_bad_parents = $wpdb->get_col( "SELECT comment_ID from $wpdb->comments WHERE comment_post_ID = $post_id AND comment_approved != '1'" );
+
+		do {
+			$children = $wpdb->get_col( "SELECT comment_ID from $wpdb->comments WHERE comment_post_ID = $post_id AND comment_parent IN (" . implode( ',', array_map( 'intval', $_bad_parents ) ) . ")");
+			$bad_parents = array_merge($bad_parents, $_bad_parents, $children);
+			$_bad_parents = array_unique($children);
+		} while ( $children );
+
+		$bad_parent_query = null;
+		if ($bad_parents = array_unique($bad_parents)) {
+			$bad_parents = implode(',', array_map( 'intval', $bad_parents ));
+			$bad_parent_query = " AND comment_parent NOT IN ($bad_parents)";
+		}
+
+		$new = (int) $wpdb->get_var( $wpdb->prepare( "SELECT COUNT(*) FROM $wpdb->comments WHERE comment_post_ID = %d AND comment_approved = '1'".$bad_parent_query, $post_id ) );
 	} else {
 		$new = (int) $new;
 	}