IEEE requires that the fonts in PDFs be embedded. After banging my head on a number of internet walls I found This Blog, which has a neat way of doing this using Ghostscript.
gs -q -dSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=tmp.pdf -dCompatibilityLevel=1.3 -dPDFSETTINGS=/prepress -c .setpdfwrite -f $1
where $1 is your input pdf.
