Some code like portfolio_googledocs_admin_upgrade_notification() in portfolio/googledocs/db/upgrade.php sent notifications to the admin. In the admin's messaging settings they can route these to a popup. I'm not sure this is working correctly. I couldn't get it to go to a popup. Maybe it's because it's a notification. Maybe it's because the sender and the recipient are the same user.

The notification is appearing in the message_read table so it's not vanishing into the void.

Replication steps:
1) log in as admin and go to your messaging preferences.
2) Set "Notices about minor problems" and "Important errors with the site" to go to popup both online and offline.
3) Grep through the code and figure out how to trigger one of these events.
4) Trigger it and see if you get a popup.

I'm not 100% sure whether the error lies in the code or in how Im attempting to trigger the event(s).