Using the command line FTP client that comes with MS XP SP2 and opening a session into a Virtual host created by virtualmin the "homes" and "domains" folders are visible but the "cgi-bin", "log" and "public_html" are not. They do not show in the file directory.
Checking the file permissions all folders have access set to 755 and are owned by the virtual host. I can not see any difference in the file permissions of the folders I can see and those that are invisible.
Looking at the folder from within linux using the domain owners password and the folders are all visible and can be written / browsed.