Epubcheck 4 is in the horizon, you should take another look at your books.
ePubcheck 4, the IDPF validator is currently in Alpha and available for download if you want test it. I downloaded it and made a first pass to what I thought was a valid book and was, not so pleasantly, surprised at how much it has changed.
I say not so pleasantly surprised because of the additonal breadth of checks the tools performs and the cryptic nature of the messages has prompted me to rethink the way in which my documents are laid out, particularly considering that I use Docbook to generate my epub content and it’s not laid out as standard HTML (uses tables to layout content wich means the table doesn’t need the same structure needed for data tables… I know… so 1990s but I did not create the stylesheets).
I’m concerned that publishers will use the new litmus test of epubcheck 4 to reject books taht would have normally passed the epubcheck 3.0.1 validation test.
The positive side of all these warnings is that documents will be more accessible because of the additional checks, assuming that authors (and publishers) bother with implementing any of the rules their books are flagged for.