I narrowed it down to this, so it isn't in default Org.
I rely on being able to put paragraphs in inline footnotes as they
were in Org 7. This implements that (and I rely on the fact that it
works well with font lock too). However, for some reason it triggers
the bug.
;; from author of new exporter, with extra \
;; (setq org-export-before-parsing-hook nil)
(add-hook 'org-export-before-parsing-hook
'hoka-org-export-par-in-inline-fn)
;; (remove-hook 'org-export-before-parsing-hook
'hoka-org-export-par-in-inline-fn)
(defun hoka-org-export-par-in-inline-fn (backend)
"Fix inline footnote paragraphs to work."
(unless (org-export-derived-backend-p backend 'latex)
(org-footnote-normalize)
;; =alpha i guess it sticks \par in there for you
(while (re-search-forward "\\\\par\\s-*" nil t)
(replace-match "\n\n"))))
