Why are my Illustrator Cs6 PDFs missing / displaying colours incorrectly?

I recently upgraded to Cs6, and since doing so have noticed the PDFs i'm ouputting are displaying terrible on both mine and clients' Macs alike. When viewed with Adobe Acrobat they are fine, but if I use any Mac native applications like Preview they are either missing elements or displaying colours are black.
Perfect example, I sent an PDF document to a client (output by CS6) and a third of the content was missing when she viewed it. For me, it displayed fine in all Adobe applicaitons.
This is happening in both RGB + CMYK modes.
Im worried that one day very soon i'm going to end up with a phone call from a client about 50,000 brochures they cannot use due to colour issues..

I find that Preview is genearally pretty lax at displaying PDF files. If they are fine in Acrobat, then it seems you won't “end up with a phone call from a client about 50,000 brochures they cannot use due to colour issues.” hopefully!
What presets are you using when exporting your PDFs?

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