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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.
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To fix this:

1. Use the Virtualmin framed layout;
2. On the left top; click on Virtualmin;
3. Open the + on "System settings";
4. Click "Server Templates";
5. On the right screen; click "Default Settings";
6. On the select box "Edit template section" choose "Apache website";
7. Find the radio button: "Automatically add appropriate SuExec directive?"
8. Choose "no", scroll down and "save".
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