I have had this issue as well, and when I changed my options to sync deleted items, this also fixed the read/unread issue. Here are the steps:
1. Go into Messages (Email)
2. Click on the thumbwheel and select Options
3. Select Email Reconciliation
4. Change the Delete On option to Mailbox & Handheld
5. Verify that the Wireless Reconcile option is On
6. Verify that the On Conflicts option is Mailbox Wins
7. Save your settings.
Happily using BES with
The Message Center Exchange Hosting