I had a quick look at the files. They are epub2 according to the internal information so the epub:type and role="footnote" items are not valid. Add in that as far as I recall, a popup footnote is restricted to 5000 characters or less (
*). Given that quite a few of your footnotes are in files over that length, they won't popup. An example is the 6986 characters for the Proteus footnote linked to the chapter 3 header.
Otherwise, the structure of the epub stinks. See the example below:
Quote:
Code:
<body class="x-ebookmaker"><div role="doc-footnote" epub:type="footnote" id="jpnote932"><div role="doc-footnote" epub:type="footnote" id="jpnote986"><div role="doc-footnote" epub:type="footnote" id="jpnote990"><div role="doc-footnote" epub:type="footnote" id="jpnote995"><div role="doc-footnote" epub:type="footnote" id="jpnote999"><div role="doc-footnote" epub:type="footnote" id="jpnote1024"><div role="doc-footnote" epub:type="footnote" id="jpnoteiot-530"><div role="doc-footnote" epub:type="footnote" id="jpnoteiot-567"><span class="c13"><em>Saint Vitus' dance</em></span>
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Add in Gutenberg's usual habits of splitting chapters between files and stuffing multiple chapters into a single file, both of which sins are committed in this abomination, using undeclared classes, an example being the x-ebookmaker used for body, a class which is never declared in either the stylesheets or inline.
I would suggest that some practice with either Sigil or Calibre's editor and plugins such as epubcheck would allow you to clean up this <expletive deleted> mess.
* See
Footnotes/Endnotes Are Fully Supported Across Kobo Platforms for more information.