The first place to start when you're experiencing large delays like that is the Exchange MTA. Unity hands all outside caller messages off to the MTA for delivery to the appropriate mailbox. check the event log for errors (RPC and RPC bind back errors are a dead give away for this type of problem, DNS issues are also common here). If there are RPC or DNS issues on the network messages can languish in the MTA queue on a box for hours or days before they're delivered to the home server. Remember that Unity is not involved in the message transport or doing any kind of syncronization... when we take a message it's delivered to Exchange immediately, we aren't hanging on to it in a proprietary DB and synching or the like.
The exception to that is if Exchange is down we home it in the local UnityMTA directory until it's up. If you're Exchange server is going up/down you'll see "Exchange off line" error messages in the applciation event log. I'm doubting that's your problem since I'm pretty sure you would have noticed that.
I'm assuming these users homed on Exchange servers off the Unity box, correct? Are the messages being delayed from outside callers or are they from internal subscribers or both? Internal subscriber delivery works a bit differently in that the message is actually originated in and sent from the sending subscriber's mailbox.
Here's a good article talking about how to troubleshoot MTA issues in general:
http://support.microsoft.com/default.aspx?scid=kb;EN-US;q247133
Jeff Lindborg
Unity Technical Lead/Answer Monkey
Cisco Systems
lindborg@cisco.com
http://www.AnswerMonkey.net (new page for Unity support tools and scripts)
