I am writing a module with a new event type, but the text in the notifications are from the notifications hook_messaging and not mine.
The problem appears to be in the notifications.cron.inc file. The function notifications_process_message does not pass the $module parameter to the notifications_message_part function calls which default the $module to ''notifications'. When I add the following line:

$module = isset($event->module) ? $event->module : 'notifications';

and add the $module parameter to the four notifications_message_part calls, my messages are used.