JAWS is the PDF maker that is built in to QuarkXPress. Like the Mac PDF maker, it has some weird quirks and problems; really, the only reliable PDF creator for press I have yet seen is Adobe Acrobat.
What font are you using? The mysterious disappearing quote mark sounds like a font encoding issue; I bet it happens with some fonts but not others. (I am assuming they are "smart" (curly) quotes that vanish; is that true?)
