[Wrongway]

I have grabbed a story from a fan site using the FanfictionDL plugin. I thought all was fine as it reads ok in the Calibre reader. However when I side load the epub to my Kobo Mini or Kobo Aura HD big chunks are missing out of chapters. I tried on a Kindle reader in mobi format and that seems fine. It seems to be the end several pages of a chapter that is missing when loaded to the Kobo. The text resumes at the start of the next chapter. I don't know if its a factor but the new chapter starts with the chapter title in the same font but larger and followed by a copyright symbol (c in a circle), and a date. As Calibre viewer shows the file correctly I dont think it's the FanfictionDL plugin or the Calibre conversion thats at fault. I am starting to suspect something in Kobo's software. Anyone any ideas?