If mailbox was added to synchronization collection by group it may be skipped from synchronization under certain circumstances. However the same scenario works if the mailbox was directly added to the synchronization collection. The following shows in Mail Source Agent log:
CADQueue::ExpandContainers TraceMsg 4504 Container '/o=Org.Name/ou=Administrative Group Name/cn=Recipients/cn=dl.name' contains x items.
CADQueue::AddChildItem Warning 4512 Skipping item ''/o=Org.Name/ou=Administrative Group Name/cn=Recipients/cn=user.name' because the item already exist in the collection 'collection.name'.
The problem mailbox was previously in a different synchronization collection. The configuration has been applied to agent database and the mailbox was in the processing queue. If now change the mailbox to a new collection by group, the group will be added to the processing queue after committing changes. But the mailbox remains in the previous collection in the queue. The problem happens as group membership will be determined only when Mail Source Agent is processing the new collection.
In Migration Manager console, locate the problem server pair, right click on it then select "Reapply Agent Configuration" to update the agent database (config.mdb).
Waiting for fix in a future release of Migration Manager for Exchange.