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you could upgrade your virtualmin version to 3.74 and see if it is better then.
It sounds like what they're seeing is a normal FTP users home directory before any files are added. With a typical FTP user, their home directory doesn't contain the website files, they'd need to go a few folders up the directory tree in order to find the public_html folder.
The other option is, when creating an FTP user, do so using the "Add a website FTP access user" button. With that, it'll make the public_html folder their home directory, so they'll immediately see the various website related files upon logging in.
-Eric