The Suexec command on your system is configured to only run scripts under /var/www, but the Virtualmin base directory is /home. CGI and PHP scripts run as domain owners will not be executed.
to solve this problem
1. install custom version of suexec
apt-get install apache2-suexec-custom
2. modify /etc/apache2/suexec/www-data
3. change first line /var/www to /home
it should solve the problem