Ref. http://talmud-wiki.org/test-of-external-links for a live demo of this bug
In the Reading Settings, my main page ( http://talmud-wiki.org/ ) points to a page with a slug “index” ( http://talmud-wiki.org/index )
As a result, any page off of the actual url ( http://talmud-wiki.org/whatever ) shows as external.
Even the page acting as the home page (http://talmud-wiki.org/index ) shows as external.
However, if I follow that with a / it works ok (http://talmud-wiki.org/index/ or http://talmud-wiki.org/index/whatever )