I have a few customers who are having similar issues regarding MWI. What is happening is the light on the phone is always lit even when all messages are read. The only way I have found to fix it is to go into the subscribers settings and refresh the MWI status.
OK, for those users, we'd probably want to start from the top and ensure that the correct Exchange notifications are arriving. In fact, I think there is a MWI macro trace that can be enabled. If you enable that, and find a subscriber currently in the troubled state, clear out all of their new voice mails if they have any. You can do this be either deleting or saving those messages. Then call into that subscriber's mailbox, leave a message and then delete it. I'd be interested to see the traces for that entire process. These would be in the AvCsMgr diag file.
You may be experiencing a known bug (CSCdz88921). I recently upgraded to Unity 3.1(5) and started experiencing this bug and the symptoms were exactly like yours.
You'll know for sure if you do not receive message store events in your diag files when subscribers get new voicemails and when they access their voicemails. Doing the steps mentioned earlier in this thread will let you know for sure.
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