If I use the fontenc package, I do not see compound numbers in the scheme:
\documentclass{report}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage[crop=off]{auto-pst-pdf}
\usepackage{chemnum}
%\setchemnum{replace-style=,format=}
\begin{document}
\replacecmpd{a}
\replacecmpd{b}
\includegraphics{test.eps}
See compound \cmpd{a} and \cmpd{b}.
\end{document}
Output:
If I comment out the fontenc package, it seems to work:
test.eps
it's impossible to say.chemnum
manual is compiled with\usepackage[T1]{fontenc}
… do you really get yellow background behind the numbers?