I have a story from a site that disagrees with my Kindle Touch. I have it set to download to mobi, but when I read to a location, it won't let me read further. Some of the text is superimposed on itself when I reach the part that won't let me advance. Any text after this point is not visible. This happens near location 525 (in chapter 6) on the Touch. I am using ver. 0.8.44 of calibre and the most current version of the plugin. The story works properly on the Touch if I reconvert it in calibre. I may have had a similar problem with another file from AO3.
Link to story:
http://www.archiveofourown.org/works/299460
Thanks for the great software.