It looks like Calibre has some bugs regarding footnotes when converting epub to azw3/KF8. When old mobi made with Calibre from same exact epub footnotes are OK, pop up windows show only one footnote. If I convert that same epub with KindleGen single footnote opens in pop up windows, same correct behavior for combo mobi file and mobi and KF8 file after splitting the combo one with KindleUnpack plugin for Calibre.
The only difference in html code that I've noticed when comparing original epub vs Kindlegen generated file (and the same case for Kindlegen KF8 split vs Calibre generated KF8/azw3) is that Kindlegen file has ID first and href after ID, as in:
Code:
Original epub:
<a href="../Text/Section0067.xhtml#_ftn1" id="_ftnref1" title=""><sup>[1]</sup></a>
Kindlegen azw3:
<a id="_ftnref1" title="" href="part0035.xhtml#_ftn1"><sup>[1]</sup></a>
Calibre azw3:
<a href="part0037.xhtml#_ftn1" id="_ftnref1" title=""><sup class="calibre7">[1]</sup></a>
And Calibre azw3 always ends up with "href first, ID second" sequence even if I reverse the ID/href in source epub. Also, I've tried editing azw3 file with Calibre book editor and after I save the changes and open azw3 file again in book editor it's again reordered to be "href first, ID second", so I can't check if footnotes would work in correct way after changing just the order of ID and href for Calibre generated azw3 book.
For Calibre azw3 clicking on some footnotes jumps to html file at the end of the book, and for some opens popup windows but shows multiple footones and a scroll bar.
Like this:
Tested on Kindle PW1 with fw 5.4.4. Of course all the footnotes are marked up the same way within the same book.
I've attached a zip of original epub and Calibre generated azw3 file, is someone want's to check on their own Kindle devices. "Napomene" in ToC = Fusnotes/Endnotes html file.