Answer
With the Manual Archiving feature introduced in MailArchiver 2012 it is possible to archive the exact same email into multiple folders.For example: A user manually archives Email-A into Folder-1 and Folder-2
When accessing MailArchiver via the web interface or IMAP Email-A is displayed in both folders.
The Outlook Connector can display an email in exactly one folder only. It will NOT display Email-A in both folders.
This is a known limitation.
As of MailArchiver 2012 IMAP is the recommended way to access MailArchiver aside from the web interface.