Do you have a file /var/vmail/domain/user/.quotausage or /var/vmail/domain/user/Maildir/.quotausage in your mailboxes? If yes, then this file is used by ispconfig to get the quota usage, its a file written and updated by dovecot.
-Yes, this is a multiserver set-up. About the permissions am NOT sure I did, as I went with the default which I guess was NOT to update permissions. (Never the less i can do this now ..)
It might be that the slave server (mail server) is not able to update the stats in the master server then. rerun the update on the mail server and choose to update permissions in master db.