The combined file is to contain the schematics & PCB layout, to avoid duplication of the mask, RFQ & build prints deselect these from the job file to leave just two selected buttons, see Output Container PDF  Combined image.

1. In the PDF section of the output containers click on Change, the window will be as per the PDF Settings  Configured.
2. Single left click on [Separate File For Each Output], select Collate Outputs Into A Single File and define the file name in the format of {Module top level number} {Module description} {PCB number} {PCB revision} then press Done. Please note that a “feature” of Altium is that should you delete the “.PDF” extension from the filename during editing you will not be able to enter spaces.
3. The settings are now correct, press OK.
4. Select Generate Content from the output container section, the file will be generated & then open in Adobe Reader (this will take some time).