Yesterday I posted the what of our problem with FND_LOG_MESSAGES, but I never explained the WHY of it. I'll rectify that right now!
In the course of our investigation we found MOS note 741087.1 which suggested that our settings for the Workflow Agent Listener Service were set wrong. Guess what? They were! This note is good to review as well to confirm the settings are correct for the FND: Debug Log profile options in your EBS application.