The two quest lines have been completed, I received the Origin achievement for both story lines, but the quests still say 0/1 at the end.
Not sure if this is a bug, or if there is more to do, but I have seen others ask about it as well.
February 2016 - last edited February 2016
Also, some guy on reddit says reinstalling the game fixed it.
Since that takes time that I'd rather be spending gaming, I hope some other fix will become available before I start that process.