I found this solution though. You need to pass the PDF that Gnuplot generated through ghostscript with the following command:
gs -q -dSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=tmp.pdf\Where 'infile.pdf' is your Gnuplot graph. If you follow the link to where I found this hack, you may notice that I have changed the commandline slightly, so that it now creates PDF 1.5 compatible output. This is a requirement of IEEE papers I think.
-dCompatibilityLevel=1.5 -dPDFSETTINGS=/prepress -c .setpdfwrite\
-f infile.pdf
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