Hi,
You are right about the color libraries. The color libraries used in QuarkXPress 7 and 8 are the updated Pantone libraries which may cause the issue.
Please change the following preference and then see the results:-
*Navigate to QuarkXPress > Preferences
*Choose Color manager
*Change the Source Setup to "QuarkXPress Emulate legacy"
Make these changes with no project open.
I hope this helps.