Have you tried exporting the same document to PDF directly from QuarkXPress rather than printing to the Acrobat Printer? If so, does that output correctly?
Also, the most recent version of QuarkXPress 6 is 6.52 which is a free download for 6 customers. There are two updaters for 6.5 so make sure you choose the appropriate version. Then you can update to 6.52. Downloads can be found here.