Rather than Print, what happens if you turn on Create postscript for later Distilling within the Export PDF settings, then use Export to PDF.
I'd set Quark PDF options to Do Not Downsample images and let Distiller handle it, beware confusing Low Quality with Low Compression.
I'm not saying this will solve anything, its just whether anything changes. I'm afraid you are a few versions ahead on OS than I'm used to. from your description it sounds like something is playing up with Distiller, have you tried creating NEW Settings files with Distiller 9 rather than importing or using one from earlier version or one amended by InDesign or Illustrator. (Robert Zacherl always said to create new with new Distillers rather than try and import, they are simple text files but although CS4 shares them each app has a few unique options). I've taken to locking my Distiller Settings files with the Finder so that I don't accidentally amend them with InDesign.
... there was the puzzle of why the sun came out during the day, instead of at night when the light would come in useful.
Terry Pratchet