First, it's a Kindle Voyage, not Voyager. Sorry, had to get that off my chest.
Generally that kind of problem is caused by formatting settings provided by the publisher. I can only guess at why copying it via USB fixed it. When you copy using USB you only get the main text file, not any of the auxiliary files that are downloaded with a book when you download it directly. Possibly the actually problem is with a setting in one of those additional files.
You should contact Customer Service and ask them to look at the formatting issue. If it is a problem with the book itself they can work with the publisher/ author to correct the problem.