Your description show clearly that you have a problem in the Webmin setting.
You can test the settings of your Webmin with the "hello word".
See tutorila video 7.
www.jms2win.com/tutorial#jms12x-7
This will help you start setup the Webmin subdomain correctly and until you are not able to access a specific document root created for this subdimain, this will not help you try setup JMS Multisites to deploy something in the specific document root.
You problem seems to show that you have all the subdomain defined like an alias of your master website that would explain that all of them reach the master website document root location.
When you will have defined the Webmin correctly for a subdomain with a specific document root location in which you only have the "hello.php" file to test the setup then you can delete the hello.php and go in the master website where you define a slave site with the new subdomain tested and its location on the disk displayed by hello world.