1. Do a clean install. Make sure the messaging defaults are correct. (email and popup permitted for everything. Email on and popup off for everything except personal messaging where popup is on when online.) 2. If possible, make a new messaging output (copy an existing one and rename?), and override the get_default_messaging_settings method to return MESSAGE_FORCED, or something. Make sure this default is used for all message type. 3. If possible, try installing a plugin that defines some new message_providers in its messages.php file. Make sure that these messages get the right defaults (from messages.php if defined there, otherwise the ones defined by the outputs.) (One way to do 3. is to go to Site administration / Plugins / Activity modules / Manage activities and use the delete link to uninstall a module that has message providers, then let it re-install itself.)