[GUI Plugin] Hyphenate This!

[bookbinder]

This is a great plugin. However, I'm having an issue :
On a certain type of file, the plugin is ONLY hyphenating text enclosed within <i> and </i> tags. The file type is azw3. The only difference I notice from other files where this issue doesn't exist is that in the files where only italicized words are hyphenated there are also footnotes (endnotes, technically). This is what the footnotes look like in the body of the text:

<sup class="calibre9"><a class="pcalibre1" href="part0005.html#foot23" id="body23">23</a></sup>

and look like this in the footnote area:

<p class="calibre6"><a class="pcalibre1" href="part0003.html#body86" id="foot86">86. Here is the footnote text.</a></p>

As you can see, this is after a Calibre conversion that created calibre classes. I've also tried this directly from the html in Calibre with the same result. I've also tried different html files with the same result. I've tried having endnotes in the same file as the body of the text, and I've tried having the endnotes in a different file. In addition, I've used Sigil to create an epub from the html, and then converted that epub to azw3 in calibre. Then I ran Hyphenate This! on the azw3 and got the same result: ONLY words in italics would be hyphenated. The rest would be full justified with annoyingly-long word spacing at times.

Any ideas as to what might be causing this??? Thanks.