When selecting "Exchange Administrative functions", "Mailbox-enable existing accounts" while running the Administrative Batch Driven Migrator, it is required to enter the hostname of the DC used to perform the function in the "Specify Active Directory Information". The actual DC specified may not be necessarily the one where the mailbox-enabling action will be performed.
In the event the domain spans multiple sites, this could not be an ideal situation if the actual DC is in a remote site as the convergence time for the Inter-Site replication might be long. Mailbox-enabled users will be displayed on the remote DC but not on the local if Inter-Site replication has not occurred after mailbox-enabling the users.
Mailbox enabling uses CDOEXM which uses the DC that the logged-on user is connected to (Global Catalog cannot be used for this task).
Change the environment variable of LOGONSERVER to be of a closer server (within the same physical site) and see if that forces it to connect to the correct DC.
An attempt to attach to a local correct server during Windows logon is encouraged to avoid replication delays.