[texhax] microtype: bad printing

[Karl Berry]

    Does anyone of you have any clue what's going on 

Not me.

    and most importantly how to avoid these troubles? 

Just maybe it would help to run the PDF through some kind of "prepress"
processor.  I've done that for some TUGboat articles for various
reasons.  Since we're already talking about bizarre behavior, just
throwing darts in the dark, but that's what comes to mind.

Here is my Ghostscript invocation (with obvious $substitutions):

$gs \
   -q -dNOPAUSE -dBATCH \
   -dEmbedAllFonts -dPDFSETTINGS=/prepress \
   -dAutoRotatePages=/None \
   -sDEVICE=pdfwrite \
   -sOutputFile="$outputfile" -c .setpdfwrite \
   -f "$inputfile" quit.ps

-dPDFX=true instead of or as well as might also do something beneficial.

All fonts "should" be embedded in the first place.  You can run the
pdffonts program (from xpdf/etc. tools) to check that.

Good luck,
Karl