Another post more for my own benefit and future reference.
epstopdf often rotates figures that you'd prefer it didn't. That's ghostscript getting a bit eager. The following kludge will fix it:
export GS_OPTIONS=-dAutoRotatePages=/None
before running epstopdf as usual.
Edit:
Or
export GS_OPTIONS="-dPDFSETTINGS=/prepress -dAutoRotatePages=/None"
to embed fonts as well...
