Does this happen regularly or just for particular users or just during specific times or anythingalong those lines?
The most common problem here is a message routing issue in Exchange or, less likely but easier to fix, a time stamp problem in a multiple exchange environment.
What version of Unity is this? Are you dealing with more than one Exchange server here?
If you do have more than one box, one thing I've seen is the classic clock problem on one of the Exchange servers - if the clock is, say, ahead an hour on the box that the message is handed off to, it wont be presented to the user (either over the phone or via the desktop client) for an hour - time stamps in the future are done for future delivery in Exchange land so it hides the message in the box. Not likely in your scenario but worth checking to be sure if you don't have all your boxes synching with a standard clock.
You can use Exchange message tracking found in the system manager for Exchange - when we leave a subscriber to subscriber message we drop the outbound message from the sender to the receiver so you can see where the message went from there. If it's left as an unidentified caller (i.e. the subscriber didn't sign in and/or call from their known phone) it's left from the Unity_(server name) account.
You can also check to see if Unity is having problems handing messages off to it's partner Exchange server - there will be errors in the application event log and there will be pairs of files hanging out in the Commserver\UnityMTA directory for periods of time - if they fail outright they'll be moved to the Commserver\UnityMTA\Failed directory - and another message should be added to the application event log.
This would normally point to, say, a DC/DNS issue or some sort of more serious network connectivity issue between Unity and the partner Exchange server.
