To reproduce the bug:
Go to Virtualmin->System Settings->Server Templates->Default settings->Mail for domain and modify "Email message to send upon server creation" selecting "Message below.."
Create a custom template go to its "Mail for domain" option and select "From default settings"
Now it may work for you as it did for me for the first time. But then not sure if it because of migration, I have migrated both of the domains to different server together with Virtualmin's settings. I need to set different settings on a new server, for example IPs, but whenever I modify "Mail for domain" for the default template it simply dies not make any effect to the custom template's email settings nevertheless "From default settings" is chosen for it. Strangely enough, instead it always takes e-mail settings from old server apparently from some temporary (cache?) file.