The problem is how one software package works as opposed to another. If you're adding more than one carriage return in your original document, the Word default is for a carriage return (enter) to be a paragraph container. So when the RTE translates that, if you have, say, 3 carriage returns at the end of a paragraph, it not only inserts the blank line at the end of the paragraph, it also inserts additional blank lines even though those paragraphs are empty.
I looked in the database at your chapters, and this is part of the markup I found.
<p dir="LTR">
What SHOULD be there is
<p>
What word is telling your document, is to RESTRICT it's format from left to right. So, somewhere in your default settings for Word, you have it it forcing all documents to left to right in format, regardless of output medium. As I've not used Word in a number of years, if I remember right, where you find this would be in your document settings. I'll check with a normal Word user to be sure.
For whatever reason, that little snippet of additional code is adding extra spaces. I removed it from the first paragraph of your newest page, and now it doesn't have all the extra spaces.