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And Calibre azw3 always ends up with "href first, ID second" sequence even if I reverse the ID/href in source epub.
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No, atributte order is not a problem. I prepared test cases that id is always first, but it does not change the result behaviour.
I suspect, that PW firmware checks Mobi headers and if it finds that a file is not created with kindlegen it displays all footnotes in popup window, instead of a chosen one.
You can check below attached test cases. kg.azw3 works fine, since it was created with kindlegen. calib.azw3 does not work properly, since it was created with calibre.