Upgrade/Update to QuarkXPress 8.01.
This behavior is occurring due to changes made in the picture import feature in QuarkXPress 7.31 (the problem does not occur in QuarkXPress 7.0 through 7.2). It is happening because QuarkXPress assumes that, if the same picture is imported into more than one box, the file information and link should be exactly the same for all boxes linked to that picture. This assumption is not true for imported multiple page PDF files. The problem is fixed in QuarkXPress 8.01