on this page the menu is not placed in a div:
<body>
<ul class="level-0" id="cssmw">
<li class="parent"><a href="#">Item 1</a>
<ul class="level-1">
<li><a href="#">Sub Item 1</a></li>
<li><a href="#">Sub Item 2</a></li>
<li><a href="#">Sub Item 3</a></li>
<li><a href="#">Sub Item 4</a></li>
<li><a href="#">Sub Item 5</a></li>
<li><a href="#">Sub Item 6</a></li>
</ul>
</li>
<li><a href="#">Item 2</a></li>
<li><a href="#">Item 3</a></li>
</ul>
Like Brian suggested, place the menu in a div and give it a high z index:
<body>
<div style="position: relative; z-index: 100;">
<ul class="level-0" id="cssmw">
<li class="parent"><a href="#">Item 1</a>
<ul class="level-1">
<li><a href="#">Sub Item 1</a></li>
<li><a href="#">Sub Item 2</a></li>
<li><a href="#">Sub Item 3</a></li>
<li><a href="#">Sub Item 4</a></li>
<li><a href="#">Sub Item 5</a></li>
<li><a href="#">Sub Item 6</a></li>
</ul>
</li>
<li><a href="#">Item 2</a></li>
<li><a href="#">Item 3</a></li>
</ul></div>
another problem is that the div for the pdf is set to use position: absolute:
<div style="z-index:-1;position:absolute;">
<embed src="File-11.pdf#view=FitH,top&view=FitV,left&navpanes=0" width="960" height="760">
</embed>
</div>
you do not set a top or left attribute though, so it will put the embedded pdf at the "absolute" top left corner of the browser window.
when using position absolute, you are in control of where the element appears in the browser, you must specify where to put it, or it will go to the default top left corner regardless of any other element that is in the top left corner.