I have had problems printing directly as PDFs from Quark.
I use this method.
First I print a postscript file using a Postscript printer driver (I use the one for my colour laser, but you can use Virtual Printer if you like).
Set the orientation of the page to be portrait and set the paper width to the width of your document.
Set the paper height to Automatic. Make sure you have the font inclusion set to 'ALL'
Create the postscript file.
Distill the postscript file using whatever settings you need to in Distiller.
This method is a bit more laborious, but it works for me every time. I can also re-distill the postscript file on different settings.
I normally use Screen or Print settings to send to clients for job approval, and then simply redistill with Press settings (or custom settings) for repro purposes.
Works a treat for the many multi million run documents I do each year.