In PDF Studio 8, attempting to add a header, footer, or watermark after running OCR on a document will result in the mark not showing up on the document.

This issue will be fixed in version 9.0 as well as in a minor release for existing version 8 installations.

In the interim, a simple workaround exists:
  1. Add an annotation to the document.  A white square or a square with no border width set will work well here.
  2. Right click the annotation and select Flatten.
  3. The header/footer/watermark can now be added as expected.