@Matt Correct. I have set org-footnote-auto-adjust to t.

On Thu, Aug 13, 2015 at 2:16 PM Matt Lundin <mdl@imapmail.org> wrote:
Matt Lundin <mdl@imapmail.org> writes:

> Gerald Wildgruber <Gerald.Wildgruber@unibas.ch> writes:
>
>> Matt, thanks! looking forward to any elucidation you can give on the
>> problem at hand!
>
> Could you tell me what the value of org-footnote-auto-adjust is on your
> machine?
>
> It seems on my end that the problem only occurs when
> org-footnote-auto-adjust is set to t. The problem seems to be line 556
> of org-footnote.el, which reorders the footnotes *after* the position of
> the footnote definition has been saved. When I remove that line or set
> org-footnote-auto-adjust to nil, the cursor is positioned correctly.

This patch should fix the issue. Testing is welcome.

Matt