You try might unzipping the epub and look at HTML files hiding inside for the defective one and the ok one and see how they differ. There is a program offered by Atlantis which makes it easy.
I suspect you will find the defective one full of unnecessary junk and the working one less so.
You can download epub-tweak by Atlantis Word Processor at:
http://atlantiswordprocessor.blogspo...-zip-file.html
This will let you open up any of the files that make up an epub very conveniently in Notepad or other text processor and make any changes you like and save them back together in the epub format. It will also let you look at them as HTML so you can see how different they are.