update-links.php is a file that does little other than to update the links link_updated times using pingomatic when it's called. However, there's nothing in Wordpress to run it at all. The trigger has to be external.
With the addition of wp-cron to the 2.1 line, the update-links.php file should be wrapped in a function with an action hook and included into the main source, so that wp-cron can trigger it on some basis.
Further suggestion: Rig the "track link update times" checkbox on Options->Misc to activate and deactivate this wp-cron job as needed. The checking timer can be set to, say, 1-2 hours or so. Add a filter to the timer so that it can be easily modified if needed. Or make it an option or something.