Of some reason Miktex 2.9 on my Windows installation refuses to embedd fonts eventhough the pdftexDownloadBase14 is set to true in the config file.

An easy fix for this is to print your document through PDF Creatorwhich will politely embed the fonts in the file it outputs! Thanks for that PDF Creator!!

Update: Unfortunately it seems that nowadays (I didn’t have this problem before) PDFCreator changes the layout of the page sightly (moving the text around on the paper) which causes the conference publishing system to reject the PDF.

The absolute simplest way seems to be to open the document in Preview on the Mac and save a copy, Preview will embed all fonts and not change the layout.

So to summarize, the way I got the PDF through the conference publishing machinery is to generate the document on windog$ with the following command:

pdflatex document.tex && bibtex document.aux

And run that command roughly four times, before LaTeX and friends has reached some kind of fix point. Now you have a document.pdf in the folder. To get the fonts embedded copy the document to a Mac, open it in Preview and save a copy, now you finally have a version with fonts embedded.