I believe this is the same bug as reported in Bug #177 (marked Resolved) and Bug #303 (still open). I'm not sure if it was ever fixed, but it is still happening for me with current versions of the software: Webmin 1.272 and Virtualmin 3.13.
When creating a new domain with FTP enabled, the domain owner account (Unix user) gets no shell and cannot FTP.
Virtualmin Module Config currently shows:
Shell for mailbox users: /dev/null
Shell for FTP users: /bin/false
Shell for jailed FTP users: None
Shell for server Unix: /bin/sh
However, as indicated in Bug #177, the "unix_shell" variable in /etc/webmin/virtual-server/config is not set. If I change the Module Config to set this value to /sbin/nologin, it does update the config file.
I know this was working on my system in the past, so somehow this value must have been reset (blanked out) in a recent Virtualmin update, or something is still broken in the module config code.