Another reason for text missing at the end of a chapter is unbalanced tags. I discovered this while reading a book where a chapter finished with the lyrics of a song. The next chapter start logically from that (he'd won the girl over with the song and the next chapter was the next morning). But, a few pages in something was mentioned that happened after the song and before waking that was important. When I opened the book in the calibre viewer, there was a lot of action after the song.
Looking at the code for the song it was something like:
Code:
<blockquote>
<p><i>Line one of yet another love song</p>
<p>Line two of yet another love song</i></p>
</blockquote>
The calibre viewer handled this OK, but the firmware stopped at the end of the song.
I wouldn't expect code like this to be generated by a calibre conversion, but there might be a bug.