It happens for every site I use, several different ones. I know the downloads are completing successfully; I can look up which ones finished in the log, and view the epubs, which are correct (and set the "Packaged" date in the preface text to today). For what it's worth one example is
https://www.fanfiction.net/s/13026532/1/
If I go to Standard Columns, none of the New Only checkboxes are selected.