My initial diagnosis from afar is the same as rashkae's. The fact that it happens on multiple books either means they are formatted the same, or there is a problem. I do have books that I know have indented paragraphs and they do not appear like yours. But, have fiddled with a couple and made them look like this before getting the indent right.
The only way we can be sure is to see the book. Any chance of that? The code that does this plus the stylesheet might be enough if you can't post the book.