In general, the Save As in Word to PDF allows the document to be as is. I found some fonts might be improved at printing time and such. But, in general, whatever is in Word is either as is, when converted to PDF, or improved. But, on that one, that is highly specific to Word, which recognizes at Print time, how to manage its file so the odd pages would be respected.

I can reproduce the behavior you describe - even when I print to a PDF printer driver from Word. It has me baffled too. You may have to save as PDF bind the scenes before printing the actual hard copy,