No visible images in PDF: MiKTeX GPL Ghostscript 9.05: Unrecoverable error, exit code 1

Question

Recently, I was forced to reinstall my MikTeX distribution. Now, in documents that compile without an actual tex error, there are missing graphics that I have included as eps-files. The following error, however, appears:

MiKTeX GPL Ghostscript 9.05: Unrecoverable error, exit code 1.

I am using pdflatex in conjunction with the auto-pst-pdf package to be able to use eps-graphics in pdflatex.

I installed the following version: basic-miktex-2.9.5105-x64, all packages were updated today. However, I have also tried the x32 version, with the same result.

Unfortunately, I am not really able to locate the problem and produce a MWE. It seems like deleting parts of the document makes the graphics appear, and, more importantly, adding more graphics makes the document not compile without an error anymore, even though I am sure that the exact same document compiled nicely when I used my initial configuration.

I have read the related questions:

auto-pst-pdf throws 'MiKTeX GPL Ghostscript 9.05: Unrecoverable error, exit code 1'

Ghostscript 8.57: Unrecoverable error, exit code 1

However, they don't mention missing images or similar things.

Any ideas on how to fix the problem?

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Interestingly, the document compiles with latex without any errors and all images are displayed. With pdflatex i don't see the images, but get the warning that the floats are way too large for the page.

In the meantime, I have also installed tex-live and other versions of miktex, all of them leading to the same error.

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As has been pointed out in the comments, auto-pst-pdf is not necessary to be able to use eps files with pdflatex. Switching from this package to epstopdf solves part of the problem: The document compiles without errors and all graphics are included. However I would like to be able to use psfrag on my figures. When I do so with epstopdf the tags are not replaced, i.e. i need to use auto-pst-pdf or pstool (see below).

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I was able to produce a MWE:

\documentclass[]{scrreprt}
\usepackage[english]{babel}
\usepackage[onehalfspacing]{setspace}
\frenchspacing
\usepackage{siunitx}
\usepackage{psfrag}
\usepackage{pstool}
\usepackage{graphicx}
\usepackage[scaled=.83]{beramono}
\usepackage[libertine]{newtxmath}
\usepackage{chemnum}
\usepackage{chemgreek}
\selectchemgreekmapping{newtx}
\usepackage{chemmacros}
\chemsetup[nmr]{
  delta = (ppm) ,
  pos-number = side ,
  use-equal,
  format = \bfseries,
  list=true ,
  coupling-nuclei-pre = { },
  coupling-nuclei-post = { } ,
  coupling-pos = sub,
 % coupling-pos-cs = \ensuremath , % <<< added
  atom-number-cs = \ensuremath    % <<< added
}
\sisetup{
  separate-uncertainty ,
  per-mode = symbol ,
  range-phrase = -- ,
  detect-mode = false ,
  detect-weight = true ,
  mode = text ,
  text-rm = \libertineLF % use libertine with lining figures
}

\begin{document}

Testing psfrag:
\begin{figure}[htbp]
\centering
\psfragfig*[scale=1.0]{./intro/test}{\replacecmpd[tag=test]{test}\replacecmpd[tag=rrr]{rrr}}  
\caption{Test}\label{fig:test}
\end{figure}

\end{document}

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It seems that chemmacros is producing the error, because if a remove it, all tags are replaced correctly. I get exactly the same error if i use auto-pst-pdf instead of pstool.

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Here is a dropbox link of all files used and created during compilation:

https://www.dropbox.com/sh/jtxchech4r20pfw/AACHdaxVNyzgQi-uT3CABFGka?dl=0