I think I see what might be the problem. When I read a book, I resize the reader window so that the text doesn't have any text from the next page barely showing. ie: the tops of the characters from the next sentence.
When I do this, the page turns work perfectly. But, when I do have some of the next sentence showing, then I start getting the results that you're getting. Also, I have found that some books just have this problem no matter what you do. I think that this is caused by the conversion that takes place to get the book into the reader.
I really don't read many books using the calibre reader, I usually send them to my Nook Classic reader. Sorry that I can't help you more than this. Hopefully, someone with a lot more experience than me will show up and point to a better way to use the reader.