Have you ever converted those books before? calibre caches conversion settings per book, so setting the necessary options might not have gone into effect.
Try:
- select all books (CTRL+A)
- click "Edit Metadata"
- check the box for "Remove stored conversion settings for the selected books"
Then try downloading the books again. The defaults set in Preferences should now take precedence, and you have already set the PDOC tag in preferences.