Not the first time this has happened but when you add a new user to the system and enable their mailbox it starts processing mail from a date in the past unless you update the "Process Email From" date to the current date, on the Email Server Profile. This is extremely risky on a live system.

I suggest that the date is automatically set to the current date, and if we wan't to process emails from before that, then we can go and change it manually to a date in the past.