It's normal for the slight delay as BES is no real-time system. Basically, there are two timers that determine when email messages are reconciled between the BlackBerry smartphone and IBM® Lotus Notes®. Both of these timers are optimized for maximum battery life on the BlackBerry smartphone. That's why read/unread marks synchronization is a low-priority task for BES Domino. The load of the BES server and network coniditions during peak hours also contribute to the delay.
RIM built an on-device function to trigger a manual reconcilation:- Messages > Click on Menu > Reconcile Now
Imagine this: 1 single user performing a "Reconcile Now" is better than BES going through 500++ BES users. Got the idea?
Link: Knowledge Sharing - BESD Wireless Reconcile timers