Turns out this was related to defining \documentclass
,\begin{document}
and \end{document}
in a \LaTeXonly
section in a comment somewhere else in the code.
Doxygen HATED that. Or more accurately the way MiKTeX reads the file or Doxygen makes the file does not allow for those labels.
So this error turned out to be caused by problems somewhere else but I had no indication of that everything pointed to this class in the log.