We had a user asking about read/unread marks not updating on their BlackBerry device. The advice from Research In Motion:
There are two separate timers in play which determine when unread marks are synchronized between the BlackBerry handheld and the Notes mail client in a Domino BlackBerry Enterprise Server. Both these timers have been optimized for maximum battery life.
The first timer is set on the BlackBerry handheld and determines when the BlackBerry will send unread marks via the BlackBerry Enterprise Server to the mail client. The methodology has changed between various handheld code lines, but from the 4.2 handheld code the BlackBerry now works in the following manner.
After the handheld has reached about 15 minutes of idle time, when the messages view is closed or when 100 changes have been made on the device, the handheld will push its changes through the BlackBerry Enterprise Server to the mail client.
The second completely independent timer runs on the BlackBerry Enterprise Server. Roughly every 60 minutes when a mail file is active (receiving email etc) the Blackberry Enterprise Server will check it for updates and queue those updates to be sent to the handheld. When a mail file is not changing we have seen this delay grow up to about 90 minutes.
In either case choosing "Reconcile Now" from the messages database on the handheld will force a check against the handheld and Notes client and reset each timer.