Aha! I bet you'd hoped you'd heard the last of me! After a long hiatus of everything working perfectly, I've managed to find another weird obscure little problem when downloading stories from FiMFiction.
There's a workaround and it's super rare, so no biggie, but I figure this might reveal some sort of underlying problem that could be worth dealing with.
http://www.fimfiction.net/story/96607/ and
http://www.fimfiction.net/story/98175/ both reported success when I downloaded them (they were listed among the "good" stories), and the text of the story was properly turned into an epub, but then when the library actually updated they were marked as ffdl_failed and most of their metadata columns weren't populated. But when I tried them again in a fresh blank default library they downloaded just fine. So I did some trial-and-error testing to see which particular difference between my library and the default was causing the failure, and I found that it was the "update calibre cover when updating metadata" option. When it's checked the problem occurs for these stories, when it's unchecked everything works correctly.
Neither of these stories appeared to have a cover image associated with it on the site, but FFDL's logs report that it's downloading cover images and in one of the stories' descriptions the author thanks the artist for an image. When I looked inside the generated epubs I found nonfunctional image files, and checking one of them out revealed that it was actually an HTML file that had been renamed as a .jpg instead. Apparently the authors mis-linked the images and FFDL choked when it tried to process them.