Kovid,
good point. Sometimes I can't see the wood for the trees and forgot to go to the obvious next step
I've just check it with a news file. It is not working on a particular book. Checking it with the editor shows a lot of warnings and some errors. Guess, I need to investigate some time with it to find out what particular is stopping the reference mode for working correct. I see there are some warnings regarding code page declaration (iso8859-1), usage of (border-width: 1) in unused css declarations, a wrong mime-type declaration and some wrong/missing picture links. Unless to say from 455 css rules are only 19 used for the book.

By the way, it is a commercial book
This story came up because of spending some time on annotations to find some odd behaviors between a Sony device and using these with different ADE versions.