(I thought we already had a thread about this, but I can't find it!) - but I've just run into the same problem with Frame 12 that I've read about other people having.
I have Frame 12, fully patched. With a book file selected (and all my chapter files open), I do File > Save as PDF,
choose the settings I want on "PDF Setup for Selected Files" dialog, and off I go.....
Those settings include the CMYK radio button.
I don't get any error messages, but loads of items are missing (blank) in the resulting PDF - mostly graphics, but also some coloured table border, text, all sorts of stuff really.
If I select the RGB radio button instead, everything is present (although I want a CMYK PDF!!)
What is going on? Is CMYK PDF generation just broken in Frame 12?
I seem to recall someone saying an imported .AI graphic was the culprit in their case, but my graphics are mostly all just PNG or PDF.