this is a long shot, but any one here tried tex4ht with animate.sty package ? When I run it by this small tex file (which works OK with pdflatex) then I get strange error. (I do have the animation frames in both eps and png, so all is there)
\documentclass{article}
\usepackage{graphicx}
\usepackage{animate}
\usepackage{graphics}
\begin{document}
\begin{center}
\animategraphics[controls,loop]{4}{frame}{1}{5}
\end{center}
\end{document}