The folder structure in Archive Manager does not match the folder structure in Microsoft Outlook and folders appear to be missing.
Archive Manager will only link a single instance of a message to the last alphabetical folder the message is found in. For example, If you have two folders in a users inbox; "A-Folder" and "B-Folder" and both of these folders contain a single duplicate message. Archive Manager will only display the "B-Folder" in Archive Manager because that was the last alphabetical folder the message was found in. The "A-Folder" would not be displayed as there are no messages in it other than the duplicate. Folders that do not contain messages will also be hidden in Archive Manager.
This is by design. If the folder is empty, the folder will be hidden by the Exchange Store Manager service and not visible on the Archive Manager website. This would also be the case where duplicate message exist in other folders with higher alphabetical names.