From what I'm reading about
that plugin it looks like it only handles the cover image of the ePub.
The ebooks I'm dealing with (Tor.com short story collections) have a "cover image" before each story. It's not a "cover image" as the epub terminology defines it.
Anyway, I completed the process manually for the ebooks I currently have by unpacking, resizing, and repacking the files with the "Unpack book" feature.