I agree that sounds like a flaw in the system. MOBI is not a robust format, and I don't know if there is a tag to identify text as a footnote or endnote. If there is then the firmware should ignore footnotes/endnotes as far as furthest page read. In a reference book, the furthest page read is almost always going to be in the footnotes/endnotes section, and you don't need to go there in most cases.
Of course even if MOBI has a tag to identify text as a footnote or endnote, there is no guarantee that publishers will use it or even understand why they should use it. Most ebooks seem to have rather sloppy formatting.
Last edited by jswinden; 09-16-2010 at 12:45 PM.