There seems to be a problem with italicized sections for fanfics downloaded from Fimfiction. Only the first paragraph of each contiguous set of italicized paragraphs is correctly italicized and the remaining paragraphs are not. Two example stories where I've found this problem are:
Mirror's Image (Chapter 20)
The Elements of Harmony and the Savior of Worlds (almost all the chapters have italicized flashback sections)
I am using FanFictionDownloader 2.1.1 with calibre 2.14.0 [64-bit].