After further research:
It appears that BB has a 20 minute or 20 things rule:
The BB syncs back with the Notes mail file after 20 minutes or 20 things happen. For instance: If you mark more than 20 messages READ then it will then sync with your local mail file. Or if you wait more than 20 minutes.
I'm waiting on confirmation from the user. But this appears to be the major problem with UNREAD / READ messages.
Here is also a BB Knowledge link which I will try next: Livelink - Redirection