I believe with a RAQ, the Frontpage extensions are enabled by the site administrator for the site. Once activated, it creates several directories, some visible, some invisible. It appears you haven't listed the invisible directories which actually contain the components that run the site. Some of these probably won't be visible within Frontpage, but should appear if you ftp'd to the site.
You could have the site administrator remove and reinstall extensions. It's best if the site is empty when installing extensions so there's less chance of conflicts.
I attempted to enable Frontpage Extensions for the site using the CP, logged in as Server Admin.
I am looking at the directory content having SSH'd into the server, so I can see everything that is there.
I haven't actually got Frontpage myself, and I've never used it - but I don't think my ignorance here is part of the problem. All I'm trying to do is use the RaQ CP to enable Fontpage Extensions on a new site.