I think in that case jk2mv doesn't reference the file and the client won't attempt to download it. I think it's a space in the file name, something like "Chicago Streets.pk3" and the client tries to download "Chicago.pk3" from the server, cause the filename gets sent over with the spaces and the client considers spaces to be seperators between files.
Thats a good point Triforce. Are you guys using an external webserver? (I didn't even document this feature but it has been there for a while now)
Removing the space in the pk3 filename fixed the issue, so it didn't have to do with their permissions, but more the issue Daggo pointed out.