[Jeff Hayden]

Wow, you're right! I've never used OmniGraffle's own PDFer and it does appear to put-out incorrect colors.

I normally use the Mac's own PDFer out of the print dialog. Go to Print and either pick the PDF or Preview drop-downs. I usually pick Preview - it outputs PDF to the Preview application so you can look at it. You can then save it from there. That output looks much closer to the Omni view.