Virtualmin might have set the default PHP execution mode for new servers to something you didn't want. 

On my system, by default all new domains will have their PHP execution mode set as FCGId (run as virtual server owner).

I want to use PHP-FPM. It was easy to change that to the default setting for all new servers. Here's all I did.

Under Virtualmin's left sidebar menu, click on "System Settings"

On the left sidebar, you'll see towards the bottom a menu item called "System settings". Click it to expand the submenu items.

Click on "Server Templates"

Now you should click on the "Server Templates" menu item. You'll be able to configure many default settings for future created servers here..

Select "PHP Options" from the Drop-down menu

In the form of the main window frame you'll see a drop down list near the top where it says, "Edit template section:".  From the dropdown, you'll select PHP Options.

Select the "Default PHP execution mode" you want

Now you'll see some radio buttons next to your choice of PHP Execution mode options. Choose the one you want and Click "Save" after making your choice.

And that's all you need to do to change the default PHP execution mode for new servers created by Virtualmin. 

As always I enjoyed writing these instructions and I hope I've helped. If you have any questions I'd be happy to answer them.