Thanks Dale. It's really a very basic file (3 heading levels and 3 body copy styles). I'm happy that the files don't look exactly the same as the ePUB as long as they are semantically the same (it still has 3 distinct heading levels and 3 distinct body copy styles). I'm just trying to establish the best way to present endnotes to Kindlegen so they work on as many Kindle models as possible.
Interestingly, I made another test file using the Indesign plug-in but this time I kept the notes as footnotes in Indesign (previously I was converting them to endnotes, which is a requirement for the print version of this job) and then the mobi file produced was okay in KP (for all Kindle models). So I guess if Kindlegen (which is what powers the plug-in I believe) converts the notes to endnotes itself it's happy but not if it is presented with endnotes to begin with. Which is bad news for me!
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