okay, here are my thoughts and I make PDFs in all versions of Quark.
Q6 has been a nightmare. I only use the postscript/distiller workflow. I know there are lots o peeps who advocate the save right out of Quark. I don't - -
Simply put, you can't control the distilling. If you are trying to make the best PDF you can, you need to be able to play with the settings at times [never recompress JPEGs - they don't play well with others].
Quark will not pick up your favorite distiller options [a good idea - perhaps in Quark 15 they will finally think of that one] so you can't set a 'perfect' distiller option and then have the save give you the results you are looking for.
Use the watched folders instead, this lets you create options you want, you create the PS file and distiller takes over from there.
Be sure to have the Acrobat Driver for Panther installed in your Library/printers/ppds/contents/resources/en.lproj folder. It is called, "ADPDF6-Panther.PPD" and is available from Adobe.
Select Adobe Acrobat as the printer type, so you don't get locked in page size and you can create whatever size you want.