These links are not working. (Here is an full example.) I suppose it should be clear why they are not, but I don’t know if it’s path problem or if it’s related to the apparently superfluous code generated in the hrefs.
I think it’s probably because of your header including <base href="http://jgoodwin.net">. I’m not sure that footnote URLs will work properly with base href, and that’s something in blackfriday. (I can think of how to fix it, but it’s Yet Another Option to Blackfriday to make it work.)