If I were to guess I'd say that the AutomaticUpdater downloaded an update N days ago, then you released a new update, then the AutomaticUpdater finished extracting and installing the now "old" update. Your user should be able to just recheck for updates and the latest update will be installed.
This behavior is by design. We do it this way to reduce overall bandwidth wasted by both your user and your servers.
Does this make sense?