Tanjamuse, it's working as intended for me, which appears to be what you describe above:
https://www.fanfiction.net/s/13439127/1/ downloads with a cover, which is different than the author's picture, as expected.
https://www.fanfiction.net/s/13430586/1/ downloads without a cover because it is the same as the author's pictures, again as expected.
If you got something different, then I suggest searching your personal.ini for errors or conflicting
skip_author_cover settings.