VirtualMin has some pesky things. Here is a simple way to revert back to the older, better way of doing things
To change from user.domain logins back to user@domain logins
Login into VirtualMin
Click System Settings
Then Server Templates
Now select the Mail for Domain template
Scroll to the bottom and change the section Format for usernames that include domain
From user.domain
to user@domain
Now you are back to normal