It doesn't appear that all accounts have been imported into ArchiveManager.
Upon checking the "Archive Active Directory Connector Service.exe.log" exceptions are visible like:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at AfterMail.DirectoryConnector.MailBoxTrustees.ProcessAccessControlEntry(AccessControlEntry ace)
Unresolved SIDs mean the accounts cannot be imported
1. Open the missing account in ADUC
2. Check the AD and Exchange Permissions
3. Remove any Access Control Entries that appear as SIDs these represent accounts that no longer exist in the Domain.
4. The next time the ADC runs, it will pick up the User. Restart the Archive Active Directory Connector Service to get this to happen sooner.