This is just after a brief look but I see a line that filters external links. Have you tried removing that line?
Granted I don't know much about the One-Page-Nav jQuery plugin but I do feel that's definitely related (I just don't know how it affects the behavior of other links).
The only other thing I'd say is in the gitHub documentation they apply a class (external) to external links when using that filter. Perhaps that's what you need to add to your external links.