Hi all (and hi Joe!)
I added a subdomain for a site, say new.mydomain.com, using virtualmin and clicking on the "Add sub-domain" option. All looked to be well, and the dir /home/myuser/domains/new.mydomain.com/ was created. Accessing new.mydomain.com from a browser resolved immediate, so I began uploading to /home/myuser/domains/new.mydomain.com/public_html/
When I access a known directory, such as new.mydomain.com/foo/index.php, it says file not found, and despite the fact that there is a valid index file in the docroot, the default page never goes away. It's as if apache is looking somewhere other than /home/myuser/domains/new.mydomain.com/public_html/ for the files, as it is behaving as though that public_html dir is empty.