Something appears to have changed between Virtualmin version 2.80 and 2.89 that prevents mailboxes from being associated to their Virutalmin user details. Everything works fine behind the scenes (i.e. mail is delivered properly), but Virtualmin does not recognize any of the e-mail settings.
For example, in the "Edit Mailbox" page, "Primary email address enabled?" is set to "No". In the "Mail and FTP Users" page, "Mail file size" is set to "None" for everyone in the domain. However, nothing has changed in the Postfix virtual table, therefore mail continues to work as before.