@Hitch: I am well aware of the idiocy of the various epub retailers that insist on using epubcheck. I keep getting bug reports about it, after all. The fact that retailers have blindly jumped on the epubcheck bandwagon does not change the fact of it's pointlessness.
@user_none: Really, you have html files with named entities that work in HTML 4 that dont work when you add an HTML 5 doctype? I would be very interested in seeing an example.