I'm going to need a lot more information. Tell me exactly what you're doing and exactly what the AutomaticUpdater is doing. Lastly, tell me what you expect the AutomaticUpdater to do.
You should know that when a user manually checks for updates (and the UpdateType property is set to Automatic) that the AuomaticUpdater only goes so far as preparing the update for installation. It doesn't forcefully shut down your app. Your update will be automatically installed on the next start of your application.
You can always forcefully install your update as soon as it has been prepared by using the ReadyToBeInstalled event.