The message that a newer version is available is a bug which is already fixed but not released yet.
I checked your example. If I use your settings, I get after conversion the following:
Code:
waiting <span class="fakesmallcaps"><a name="RETN1">CATSA</a><sup><a href="#_EDN1" id="_EDNREF1" title="">[1]</a></sup></span> agents
and the endnote:
Code:
<p><a href="#_ednref1" id="_edn1" title="">[1]</a> <em>Canadian Air Transport Security Authority </em></p>
This is as it should and would work as designed. The additional anchor (RETN1) could be deleted if you do not use it manually or automatically by activating the option 'remove bookmarks' in the HTML Conversion settings.
I could not explain why you got a dollar sign in the cover page. I literally created more than two hundred books this way and never got a dollar sign. However, I figured it out. You are using a PNG as a cover image instead of a JPG. And indeed I made a typo for the PNG cover. This is corrected and will be published in the new version soon. Thanks for the bug report!