Also, I have problems with equations even when I use \(...\) instead of
$...$.

This, for example:
--8<--
* example
Example[fn:note].
[fn:note]An equation: \(\bar{a}\).
---8<--

becomes this:

---8<---
Example\footnote{An equation: \(\bar\{a\}\). }.
---8<---

I'm not really sure, but I suspect this worked before I instaled the latest
version of org-mode.

Sorry for any inconvenience.
--
Rafael Calsaverini
Dep. de Física Geral, Sala 336
Instituto de Física - Universidade de São Paulo

rafael.calsaverini@gmail.com
http://stoa.usp.br/calsaverini/weblog
CEL: (11) 7525-6222
USP: (11) 3091-6803