There is probably a very simple explanation for this (hoping). I appreciate hearing from anyone who may understand the issue.
The second level sidebar menu links work correctly when you first select a secondary page, however, once on that secondary page, when you click on another secondary link, the link is broken. It appears to be an issue with the URL as a # is added. See example below.
Example of functioning link:
http://domain.com/page-1
Example of broken link:
http://domain.com/page-1#page-2
<div id="sidebar">
<ul id="subnav">
<% control Menu(2) %>
<li><a href="$Link">$MenuTitle.XML</a>
<% if LinkOrSection = section %>
<% if Children %>
<ul>
<% control Children %>
<li><a href="$URLSegment">$MenuTitle.XML</a></li>
<% end_control %>
</ul>
<% end_if %>
<% end_if %>
</li>
<% end_control %>
</ul><!-- #subnav -->
</div><!-- #sidebar -->