jackie_, thank you for your technical analysis. I've dived into a fixed kepub and found that Modify ePub left something in the XML that should have been removed.
Code:
<?xml version='1.0' encoding='utf-8'?>
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
<title>Wild Cards I</title>
<link rel="stylesheet" type="text/css" href="../styles/stylesheet.css"/>
<style id="kobostylehacks" type="text/css">div#book-inner p, div#book-inner div { font-size: 1.0em; } a { color: black; } a:link, a:visited, a:hover, a:active { color: blue; } div#book-inner * { margin-top: 0 !important; margin-bottom: 0 !important;}
</style><meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
</head>
The above is a header from an XML after Modify ePub was run. The bit in bold is what's left behind. With that gone, things work much better. This is a set of styles that does modify the way the XML looks and without it, we are good to go.
There is one other difference, if the original ePub containes the file page-template.xpgt, that does get stripped.