It could be. I almost never create EPUB from book files.
What happens if you make an EPUB from just one chapter? Does the same thing happen?
If it's only from the book file, report the bug here:
Thanks Steve - making the ePUB from one chapter works as expected. I have logged the bug report, as you suggest.
Answering my own post
I was contacted by one of the Adobe team responsible for epub output and he put me right on this issue.
In Book files, there is the concept of a Style Source - that .indd file contains all of the styles for the book and is used to copy all of the styles to the other chaters in the book. When outputting to an ePUB (and, I guess, a PDF file) form the Book file, then the styles in that .indd file are used across the project.
In my testing, I had shortened the class names for each of the styles in the constituent chapters except in the source file, so the original class names were being used for each of the HTML files being output to the ePUB. Once the source file had been updated, then the output worked as expected.
Great. I'm glad you got a quick answer on that.