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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:

Reto Höhener
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    Well, without test.eps it's impossible to say. – egreg Nov 01 '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 01 '15 at 15:45
  • sorry no the yellow background is my own emphasis (made with greenshot) – Reto Höhener Nov 01 '15 at 15:46
  • ChemDraw and eps files: http://dropcanvas.com/i56ly (temporary I guess). The eps file I created by saving as *.eps from ChemDraw. – Reto Höhener Nov 01 '15 at 15:51
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    @Zalumon your example compiles fine for me and all numbers are there… – cgnieder Nov 01 '15 at 15:53
  • @clemens tnx a lot for testing... that's unfortunate, as it means I have to go hunt in my texstudio settings (maybe it's because I use output-directory). Edit: no, removing the output-dir setting didn't help. – Reto Höhener Nov 01 '15 at 15:58
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    Do you have the cm-super fonts installed? – Ulrike Fischer Nov 01 '15 at 16:18
  • @UlrikeFischer it didn't look like I did, meaning it was possible to select it in the package manager and install it (which I now just did). Unfortunately that didn't help :/ – Reto Höhener Nov 01 '15 at 16:35
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    Are the fonts used? (See at the end of a pdflatex compilation). – Ulrike Fischer Nov 01 '15 at 16:38
  • @UlrikeFischer I am still struggling to verify that cm-super is installed and used. I don't really see the package on the file system and I also don't know what to look for in the output. I assume you mean the log file. – Reto Höhener Nov 01 '15 at 16:48
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    Make a small example with [T1]{fontenc}, compile with pdflatex and then look in the log file which fonts mentioned at the end (.pk: bad, .pfb: good) – Ulrike Fischer Nov 01 '15 at 16:52
  • @UlrikeFischer doesn't look good: MiKTeX\2.9\fonts\pk\ljfour\jknappen\ec\dpi600\ecrm1000.pk (took me so long to investigate because the log line was hard-wrapped right between the 'p' and the 'k', so my search always came up empty for both .pk and .pfb) – Reto Höhener Nov 01 '15 at 17:06
  • btw, I did find the cm-super files: C:\Program Files (x86)\MiKTeX 2.9\fonts\type1\public\cm-super (> 400 files, ~60MB) – Reto Höhener Nov 01 '15 at 17:07
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    Run on a command line updmap. – Ulrike Fischer Nov 01 '15 at 17:12
  • wow. now I get: <C:/Progra m Files (x86)/MiKTeX 2.9/fonts/type1/public/cm-super/sfrm1000.pfb>. And the chemnum issue is resolved as well. Thank you very very much! This cost me my whole sunday. Pls convert to an answer and i'll be happy to accept. – Reto Höhener Nov 01 '15 at 17:20

1 Answers1

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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.

Ulrike Fischer
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