I am on Indesign CS5. I have managed to make an ebook that is perfect apart for one thing:
the footnotes do not take me to the desired note, but to the last pages of the final chapter. If I browse a few more pages then I can see the note. Clicking on the note number then neatly takes me back. Apparently Indesign sees no division between the end of the chapter (or of the book) and the starting of the footnotes.
(NB: I already use the Teus de Jong script to against the footnotes/crossrefs bug).