It sounds like you are printing and distilling to get your PDF. That is no longer a recommended workflow and you should be Exporting to PDF instead, but if there is some reason you must use distilled PDF, make sure you click the setup button in the Print dialog to enter the print driver settings and check the include blank pages checkbox.
the PDF preferences say export 'direct to PDF'. The other option is 'create post script file for later distilling', but that on is unchecked.
But you go to create a PDF to the print command.
But you should take File > Export > PDF (Print).
Never create a PDF via print, avoid postscript in any way, no EPS, no Distiller, nor File > Print to PDF.
Please show us the dialog where you see these options....