Read/unread sync is never immediate unless your BES has only 1 user to serve. It is a low-priority task and it is not unusual to have to wait up to 20-30 minutes for them to sync. That's why all 4.0 & above BB have the messages option "Reconcile Now..." - your users can use this function to request for an update sync to be performed; but again it will work or not work depending on:
1. BES server load
2. user's mail server availability
I would not see this as a very critical issue but I will be more worry if email messages are not redirected to BB...
Native but 4th class citizen of a nation governed by idiots who import congestions & contention.