Email functionality was disabled. When email functionality is disabled in Agile Central, the system only requires the username, which it calls "EMAIL ADDRESS".
If a user logs in via SSO with a username that is different than their previously-set email address in Agile Central WHILE email functionality is disabled, the System User will update the username (EMAIL ADDDRESS) with the username provided as the SAML subject via SSO. This is because the system is using only this one field - and the SSO credentials provided map to the same user, thus the system updates the username to match.
When Email Functionality is re-enabled, the username is copied to the email address by the system, and thus displayed.