I did yell "victory" too soon - tried again this morning, had the problem again with another story.
http://archiveofourown.org/works/695705 => Opens
All Shall Return to Light - bobbiewickham.epub
http://archiveofourown.org/works/3473315 => Doesn't, like the previous ones I linked; but opens if I download it directly from AO3
Elama - shakeskp.epub (dl with fff)
Elama.epub (dl from ao3)
I did let my reader update; I even tried a hard reboot and re-updating it at first when I realized there was a problem, and used the Kobo app just in case. It didn't change anything, that's when I started looking at the problem more closely, and it looked like it came from FFF.