Solution 1:
Update to QuarkXPress 9.5.1. Any newly created projects will not exhibit this behavior.

Solution 2:
If you have already saved projects that exhibit this behavior, you can follow these steps to fix them:

  1. Create a new project in QuarkXPress 9.x using the default settings.
  2. Navigate to File > Append and select the original file.
  3. Select Layout from the list of Append items on the left of the dialog box.
  4. Highlight the layouts you want to append in the Available field.
  5. Import the selected layouts into the new project.
  6. If you don’t want to use the Default layout, go to the Default layout and delete it.
  7. Save the project.

Solution 3:
Sometimes permissions or privileges are set incorrectly on a server volume at the time a QuarkXPress 9.0 - 9.x project is saved to a folder on your file server. In this case your best option is to update to QuarkXPress 9.x and do a Thumbnail drag of the project. To do so, follow the thumbnail drag procedure described in Knowledge Base Article - 'How to Perform a Thumbnail Drag'.