Did you ever get to the bottom of this? I have a similar issue with Layout 2016 on a Mac - printing directly from Layout or an exported pdf of the same file shows coloured fills as half tones and the bounding boxes of fills reducing the quality of anything within them e.g. lines, text. On screen, the pdf is fine. I have found that if I open the pdf in Adobe Reader and print from that (rather than Apple's Preview) it prints fine, but that’s adding to the workflow.