The root of the mailbox in the Archove Manager website is a representation of the MailboxMessage table in the database. This is a collection of all mail items that have been associated (linked) to a mailbox.
The number of items linked to the root of the mailbox will represent all items that are linked to that mailbox regardless if those items are linked to a folder within that mailbox. This means that the sum of all the items in each folder in a given mailbox will be equal to or less than the total number of items linked to the mailbox.
The Archive Manager Exchange Store Manager service (ESM) is responsible for linking items that it finds in the Exchange mailbox to the corresponding folder in the Archive Manager mailbox. Items that are linked to the root of the mailbox and are not linked to a folder were not found by the ESM service but were rather linked by the Journal Report Data Loader (JRDL) or the Mailbox Maintenance SQL job (in the older versions).
Keep in mind that the Archive Manager mailbox is not a direct reflection of the mailbox as seen in Outlook. Refer to this KB for additional information: https://support.quest.com/archive-manager/kb/55689
Messages linked at the root of the mailbox does not represent an issue with Archive Manager, and is part of normal operation of the software.
