Its one thing to have an FTP user, and its another to browse the files on the web through HTTP. You have to tell the web server where the files are and what hostname and path they are served under.
When you setup a domain or a subdomain like http://username.example.com/, you specify a "Web directory" - if each user is to have his own subdomain, then you need to make sure you have this set correctly.
If the user is to have files served from a path, like http://example.com/users/username/, then you need to use the "Re-map Sub-dir" function in the Web Admin Panel to tell the server that files for that path are in that user's directory.
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