Groundspeak (company behind Geocaching.com) has published a new API. Authenticating to their functionality is only valid for 3600 seconds (or 1 hour). If the application does not refresh this login, it will expire and you'll be forced to login via their site. The background notification process forces a refresh, even if the validity has passed as this has some extended period. Most of the times this allows the background process to continue, while using the application this isn't done. That is a security measure. Unfortunately not all users prefer this kind of behaviour. The next version will have the option to switch to less secure behaviour.
To check if notification is still running, choose 'Help | Details' and check the history if all are OK. To check if there are any errors, choose 'Settings | Other ... | Log to file' to activate logging and 'Help | Log file' to check for errors. The slider can be used to filter out debug, info or error level messages.