I'm glad you posted this. I have the same problem and changing the chapter break options does nothing. Using ePUB books of course.
So far, this has happened mostly with Baen books (especially the Honor Harrington novels - in the free library if anyone wants to try). I suspect it may have to do with some obscure flag in the book conversion itself that makes only this app hiccup (FBreader, Coolreader and my Nook (the actual Nook, not the app - haven't tried that) are just fine with these files, as is the Calibre ebook viewer).
By the way, in my case, this happens for ALL chapters (i.e. a large chunk of text gets cut off before the next chapter begins).
Here's an example book from the Baen free library -
http://www.webscription.net/p-92-crown-of-slaves.aspx. If you have a free/public domain book that you're seeing a problem with, I'll be happy to test it too so we can make sure it's not some setting that's at fault.
Edit: changing the chapter break size from 50K all the way to 5000K (in several steps) did
not change where the text broke for me (this seems different from what you saw).