Sounds like a permissions problem to me. If you haven't run the Permissions Wizard on the new mail stores before moving users over, they won't work properly. Secondly, it may take some time for the sync to complete between domain controllers, and from the domain controllers to Unity to reflect the new mailbox location. For starters, re-run the PW(logged in as a domain admin) on the new mail stores where users will exist, and then give it some time to settle once the mailbox is moved.
Let me try to clarify what Brad is telling you by giving you a step by step process to follow. It is fine to add whatever storage you want and whatever mailstores you want and move whomever you want to those stores. Unity however will not work on those mailboxes until you do the following.
Run the Permissions Wizard on Unity. In the step that has a button that says Choose Mailstores, you have to put checkboxes on the new mailstores to give Unity the ability to access them and process them for messaging and MWI functions. Please run the permissions wizard after you have added the new storage and stores and choose those stores to enable Unity permissions on them or they will not function properly.
The user in his post also mentioned different domains - in the permission wizard, make sure you are including all domains in the domain section of the permission wizard. I also recommend using the root level to ensure all OUs are included, not just Users OU, for example, use xyz.com instead of xyz.com/users, otherwise Unity may not work when you move a user from the Users OU to a different one, very common in AD deployments. Also should mention, as long as the Unity service accounts are the same for all Unity servers, you only need to run the Permissions wizard for those accounts (plus don't forget delegation of control wizard for the Exchange servers).
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