That’s certainly a mouth full. We stumbled on this weirdness when working on PDF Importing for our iCatalog Editor. I am filing this as a Mac bug at the same time as communicating with DTS to see if they can offer a workaround for this problem.
The problem appears if a PDF is using a CMYK color blending space on a page for transparency blending. That causes this effect. Left side is how the PDF comes out on Mac, right side how it looks correctly on iOS (Simulator/Device). Also if you view the PDF in Preview or Pixelmator it looks weird, only in Adobe’s tools do they look correct.
If the behavior were the same on Mac and iOS then I would have thought to be Adobe using some weird special extension, but since the output is correct on iOS we think that this must actually be a bug. Maybe the Mac version of Quartz PDF rendering tries to do something smart since it is aware of color calibration but doing so messes up the colors.