How can you know that
3.6 has 6 "phantom" books that dont get updated without knowing what they are??
Without details such as story URLs to check or even the site that you're having problems with, all I can suggest to you is the usual restart(calibre)-reinstall(plugin)-reboot(OS) dance.
And yes, FanFicFare is purely a client application. Prior versions are available in the
github repo.