I learned that you should not combine pdf files with different pdf versions. They can be converted by reinterpreting them in ghostscript, as below.
gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4
-dNOPAUSE -dQUIET -dBATCH
# In windows, replace 'gs' with 'gswin32c.exe'
that made the trick for me. It's trivial to call ghostscrip with 'exec' or 'system' from perl.
It wasn't a perl problem and I should not have posted it in perlmonks, probably, but I wanted to share the solution anyway.
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