When you add a domain, SmarterMail automatically creates a domain alias for the "mail." prefix. For example, if you create a domain with the name "example.com", SmarterMail internally creates a domain with the name "mail.example.com".
If you happen to create two identical domains in SmarterMail (one with the "mail." prefix and one without), the domain with "mail." may disappear from the domain list as SmarterMail believes it is the automatically created alias. Therefore, only use one domain without the "mail." prefix and rely on the automatically created alias to properly route mail.