I haven't used Quark in years, but I know that you're not exceeding any sort of pdf file limit. It could be a bug in Quark Xpress or a problem with the font itself. The latter would be my guess. I would try uninstalling and the reinstalling the typeface in question and then seeing how the pdf displays. Maybe a Quark user will jump in - I've used InDesign since version 2 and in the CS6 version and versions past, has done an excellent job of exporting pdfs.
It would be nice to know what platform you're on and whether the font in question is OTF or TT.
Regards,
Clinton