Index: wp-admin/includes/upgrade.php
===================================================================
--- wp-admin/includes/upgrade.php	(revision 26003)
+++ wp-admin/includes/upgrade.php	(working copy)
@@ -1303,8 +1303,10 @@
 	}
 
 	// 3.5
-	if ( $wp_current_db_version < 21823 )
+	if ( $wp_current_db_version < 21823 ) {
+		remove_all_filters( 'default_site_option_ms_files_rewriting' );
 		update_site_option( 'ms_files_rewriting', '1' );
+	}
 
 	// 3.5.2
 	if ( $wp_current_db_version < 24448 ) {