Hi Kenneth,
Could you clarify what you mean by "During the user migration process we do change the pointer in Unity to their mail file on the new Domino server"? Typically when moving a user's mail file to a new Domino server, Unity should automatically pick up those changes. Are you pehaps creating a new mail file and pointing Domino to it instead of moving it? If that is the case, the new mail file would not have been DUCS enabled, a process it must go through before Unity will be able to access it properly. The only way to force that to happen would be to reimport the user into Unity. If the mail file is properly migrated, however, the mail file should remain DUCS enabled and there would be no need for this.
An easy way to determine whether the user is DUCS enabled is using the DUT tool. It is located on the Unity server under \Commserver\Utilities\Domino\DUT. It will show you a list of all of your users. Compare the values you see in the UCProfile section for a working / non-migrated user to a failing one. You might also want to verify that it lists the updated mail server and mail file for the user.
Also, while I don't think it would cause this particular problem, you should be aware that Server 2008 is not currently a supported platform for DUCS/CsServer 1.2.5, see page 6 in the admin guide:
http://www.cisco.com/en/US/docs/voice_ip_comm/unity/duc/admin/guide/cuducag.pdf
Hope this helps,
Pat