Despite Powershell being setup correctly and being able to sucessfully Mailbox Enable users using Quest Notes Migrator for Exchange (NME), when attempting to Migrate Data the Administrator is prompted with a "User has no mailbox" error message whilst running the pre-migration checks.
AD replication was not running between Root and Child Domains, NME was using the Domain Controller (DC) and Global Catalog (GC) Servers from the top level domain but these servers were not being updated and NME was unable to locate the User Mailbox objects.
Once the AD Replication issue was diagnosed using Microsoft's repadmin tool, the issue was resolved after AD replication had occured between Root and Child Domains and the GC/DC was updated. NME could then find the Mailbox enabled user objects and successfully Migrate Mail data.
In one customer secenario it was found that AD replication was not running from the Root Domain to their Child Domains. This issue was diagnosed while trying to create a new Migration Account with the correct Exchange rights. Upon creating this account the AD Administrator was prompted with a message that replication has not occured.
Information about the Replication Diagnostics Tool (repadmin): http://technet.microsoft.com/en-us/library/cc755360(WS.10).aspx