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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:

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15
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    Well, without test.eps it's impossible to say. – egreg Nov 1 '15 at 15:44
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    The chemnum manual is compiled with \usepackage[T1]{fontenc}… do you really get yellow background behind the numbers? – cgnieder Nov 1 '15 at 15:45
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    @Zalumon your example compiles fine for me and all numbers are there… – cgnieder Nov 1 '15 at 15:53
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    Do you have the cm-super fonts installed? – Ulrike Fischer Nov 1 '15 at 16:18
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    Are the fonts used? (See at the end of a pdflatex compilation). – Ulrike Fischer Nov 1 '15 at 16:38
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From the discussion in comments the source of the problem was that the cm-super fonts were not installed and so bitmap fonts were used.

In miktex the fonts can be installed with the package manager. In some installations it is necessary to run the command updmap after the installation to update the user map files.

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