There is a link resolved that is dropped back into the queue for the Directory Synchronization Agent to process at a later time. The next time a migration is ran with the second batch of Users, replication has occured and the Group is now on the GC, and the unresolved link in the queue gets resolved, and the membership is updated correctly.
Set the values of the preferred Global Catalog and preferred Domain Controller to the same Server to eliminate replication delays. This allows the group to be created and membership to be updated correctly.
Refer to Solution 14630 - "Specifying preferred Domain Controllers for the Directory Synchronization Agent" for information on how to specify preferred DC and GC: