The problem is the <base href=......> tag that is auto-stripped into the header, that will prefix all hyperlink URL's.... unless you hard code the full URL.
You have to HARD CODE the full link with the page ID into the bookmark links.
Try this, (where your page ID is your ez-page ID NUMBER - in my case it's 22, and the URL is your website URL):
<p><a name="Top_of_Page">Top of Page</a></p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#A.">A</a></p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#B.">B</a></p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#C.">C</a></p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p><a name="A.">A.</a><br />
Aaron, Alan, Angus Arnold, </p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#Top_of_Page">(Return to top)</a></p>
<p> </p>
<p><a name="B.">B.</a><br />
Barry, Bert, Brian</p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#Top_of_Page">(Return to top)</a></p>
<p> </p>
<p><a name="C.">C.</a><br />
Cedric, Clive, Colin</p>
<p><a href="http://www.YOURWEBSITE.COM/index.php?main_page=page&id=22/#Top_of_Page">(Return to top)</a></p>