I can reproduce this with a simpler document:
--8<---------------cut here---------------start------------->8---
\documentclass{article}
\usepackage{amsfonts}
\begin{document}
\begin{equation}
x
\end{equation}
\end{document}
--8<---------------cut here---------------end--------------->8---
and this manifest
--8<---------------cut here---------------start------------->8---
(specifications->manifest
(list
"texlive-base"
"texlive-amsfonts-fixed"
;; "texlive-latex-amsmath"
))
--8<---------------cut here---------------end--------------->8---
--
Ricardo
