Missing mailboxes in Mailbox Activity Summary Report when it has been confirmed messages have been sent or received by those mailboxes
The Mailbox Activity Summary report data is populated using date from the Exchange Tracking logs. If this information is missing from the gathered tracking logs, or if MessageStats is not gathering all tracking logs then mailboxes with Sent and Received data will not show up in this report.
Ensure MessageStats is gathering all of the Tracking logs from each Exchange server that contains this information. You may need to check that the correct MessageTracking directory is shared on those servers: