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I'm pleased to hear that it's not just me that is suffering this problem then! I have raised it as an issue with the Support Ninjas and they are looking into it through engineering. We tried a few tricks involving Apple's ColorSync Utility but it made no real difference to the problem.

The only other information that I can add is that I have tried opening the resulting PDF export in every other application that I can find capable of reading a PDF file and only Adobe Reader and Safari display the colours incorrectly. PDFs from every other application appear to be rendered correctly by everything.

Let's hope a solution is found soon as it's the only annoyance I have found with OmniGraffle - and I use it a lot these days. It's a problem to me as 99% of my drawings end up being read on PCs through Adobe Reader.