Hi there. I just tested this on the current codeline and it's working as documented for me, so you may have a missing piece of the puzzle. A simple test is to drop a new HTML instance on a page. Go into the editor's Source view, and paste in the following HTML, consisting of the default accordion and its associated custom JavaScript. When you save and view the page, the accordion should appear fully collapsed. You mentioned changing the Layout Master to include the JavaScript portion? One suggestion I have is to select View, Source, and make sure that the JavaScript is appearing where you are expecting it to. The most important thing is that the class names match between the accordion div and the JavaScript.
<p>Paragraph before the accordion</p>
<div class="collapsed-accordion">
<h3><a href="#">Section 1</a></h3>
<div>
<p>Section 1 content.</p>
</div>
<h3><a href="#">Section 2</a></h3>
<div>
<p>Section 2 content</p>
</div>
<h3><a href="#">Section 3</a></h3>
<div>
<p>Section 3 content</p>
</div>
<h3><a href="#">Section 4</a></h3>
<div>
<p>Section 4 content</p>
</div>
</div>
<p>Paragraph after the accordion</p>
<script type="text/javascript">// <![CDATA[
$('div.collapsed-accordion').accordion({active:false, collapsible:true, autoHeight:false, fx:{opacity:'toggle',duration:'fast'}});
// ]]></script>
I hope this helps,
Jamie