How can I verify that the extraction tools are actually showing all mailboxes? It seems as though some are missing from the reports.
I am assuming that you are using msextmz.exe / msextmzcfg.exe. The tool will look at 3 properties on the mailbox and optionally look for at least one recurring meeting organized by the user. If none of these return a hit, then the user will be noted in the output.txt (or nonexistent.txt) with no entry.