Index: wp-includes/default-filters.php
===================================================================
--- wp-includes/default-filters.php	(revision 21526)
+++ wp-includes/default-filters.php	(working copy)
@@ -282,4 +282,7 @@
 add_action( 'admin_init', 'register_admin_color_schemes', 1);
 add_action( 'admin_color_scheme_picker', 'admin_color_scheme_picker' );
 
+// If the upgrade hasn't run yet, assume link manager is used. 
+add_filter( 'default_option_link_manager_enabled', '__return_true' );
+
 unset($filter, $action);