Okay, found something else:
the expression (.*) is not capturing strings that are longer than one line of code. For example:
a search for
Code:
<div[^>]*>(.*)</div>
comes back with zero hits, even though there are multiple instance that should be matched by that, such as:
Code:
<div class="s1">
<h4 class="calibre3" id="heading_id_2"><span class="none">Chapter 2.</span></h4>
<h4 class="calibre3" id="heading_id_3"></h4>
</div>