Index: src/wp-admin/includes/schema.php
===================================================================
--- src/wp-admin/includes/schema.php	(revision 41337)
+++ src/wp-admin/includes/schema.php	(working copy)
@@ -1059,6 +1059,7 @@
 		$current_site->site_name = ucfirst( $domain );
 		$wpdb->insert( $wpdb->blogs, array( 'site_id' => $network_id, 'blog_id' => 1, 'domain' => $domain, 'path' => $path, 'registered' => current_time( 'mysql' ) ) );
 		$current_site->blog_id = $blog_id = $wpdb->insert_id;
+		update_network_option( $network_id, 'main_site_id', $blog_id );
 		update_user_meta( $site_user->ID, 'source_domain', $domain );
 		update_user_meta( $site_user->ID, 'primary_blog', $blog_id );