I came across something similar the other day,
placed a landscape pdf into a landscape layout, 3 times in different positions each into zero degree rotated picture boxes.
printed to landscape media but 2 of the picture boxes came out with the content rotated 90 degrees, so completely different crops.
My result was nothing to do with quark as I was using InDesign CC and the XMPie Dynamic Print command to output to pdf.
My Fix was to clean up the placed pdf by place into InDesign once and Export to a cleaner PDF.
I believe that when you change the page rotation of a pdf to view it in Acrobat Pro, this is saved as a flag in the code (rather than actually rotating content), In my pdf workflow I have a checkbox as to whether or not to honour Acrobat Page Rotation
. I'm guessing that my original pdf had this rotation checked and placing into InDesign reads it but printing out to pdf (again assuming XMPie uses an interim postscript stage (just like Quark)) ignores the flag.
lots of assumptions but it might help ?