Exchange sites (in Exchange 55 I assume) cannot be spanned with a single Unity server. This is a limitation of the Exchange MAPI security implementation (i.e. there's no easy way for us to log into mailboxes in a different site using the service account on our local server).
Using Exchange 2K and AD you can include users across mutliple domains on a single Unity server. You need to be sure to have rights setup on the containers where users are stored in each domain (the Unity Permissions Wizard available on CCO or AnswerMonkey can help with this).
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