Some time ago1, I noticed that the Org footnote mechanism was not working correctly. As with similar footnote facilities, you add a footnote by marking where you want the footnote to appear in the text and then adding a paragraph starting with the same marker that contains the text of the footnote. Usually, you add the footnote definition in the next paragraph so that the definition is near its reference in the text. For example, the text generating the above footnote is
Some time ago[fn:1], I noticed that the Org footnote mechanism was not… [fn:1] Most likely when I upgraded to Org Mode 8.
Org is supposed to collect the footnotes and put them at the end of the page on which they occur. Instead, the footnotes were being added at the spot where they were defined. Org mode is under constant development so I assumed, as I had with Magit, that one of the updates introduced the error and that it would be fixed the next time I updated. In the meantime, I just moved the footnote definitions to the end of the text.
When I finally got around to updating however, the error was still there. So I did what I should have done originally: I read the manual. It turns out that somewhere along the line Org was updated to require two blank lines after the footnote definition. That was presumably so that you could have a multi-paragraph footnote. Once I added to second blank line, everything worked correctly.
As geeks, we're fond of invoking the RTFM mantra but sometimes we forget it ourselves. Anyway, this post is a heads up to anyone who is experiencing the same problem.
Most likely when I upgraded to Org Mode 8.