How to exclude transparent areas in Image Trace

I have a logo file, saved as PNG, that is black on transparent.  Very simple file, just stylized black lettering on a transparent background. In Illustrator CS5, I can place that file, do a "Live Trace" in "Lettering" mode, and Illustrator will correctly ignore the transparent areas when I expand the trace.  After expanding, I'm left with scalable paths and an easy way to change the fill color to have the logo work with my background.
Fast forward to Illustrator CS6.  I try to do the same thing but a) there is no "lettering" preset for Image Trace and b) there is no setting I have yet found to cause Illustrator to ignore the transparent areas when I expand.  If I then fill, everything inside the bounds of the placed image (the square containing the logo) is filled with that color.  The only way I've found to get similar results is to go through the layers panel after the Expand and deselect each piece of the image that should not be filled.  I have a hard time believing this is the desired approach.
I freely admit that I'm an Illustrator novice and I suspect that there is something one of you Illustrator experts thinks is obvious that I'm missing.  I'd sure appreciate some guidance in the right direction.

I doubt that the Trace feature in CS 6 is a big improvement to CS 5
Here look what might help you with this you might even be able to do a better job in Photoshop.
I'm using your screen shot so the trace is not a good one but shows you the steps you can take to make this work better.
Even though it is an image you can edit the colors some what here I went to Edit>Edit Colors>Adjust Color Balance ad turn the Cyan down to "0" and move the black slide a bit higher as well.
The I did my trace and remove the clipping paths there are 2 clipping paths the way you remove the path and compund path for the square is to select one edge of the psth with the direct select tool, you need smark guides turned on to see the paths.
the hit delete and the hit delete again and repeat for the second compound path as such path willpreven the sqaure to becoming a background filled path.
It should be noproblem filling this without a Live Paint Group it is just that you are not familiar with what is happening to the art.

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    aside {
        padding: 0 2%;
        float: left;
        width: 30%;
    footer {
        clear: both;
        background: #B00202;
        color: #FFF;
        text-align: center;
        margin: 0;
    /**typography**/
    header h1, header h2 {
        display: inline;
        color: #F5DD83;
        padding: 0 1%;
    h3 {
        color: #2294AE;
        margin-bottom: 0
    p { margin: 0 0 1em 0 }
    figcaption {
        text-align: center;
        font-style: oblique;
        font-size: small;
        color: #2294AE;
    </style>
    </head>
    <body>
    <!--begin header-->
    <header> <h1>Sitename</h1>
    <h2>|  Responsive CSS Layout</h2>
    </header>
    <!--begin navigation-->
    <nav>
    <ul>
    <li><a href="#">Menu Item1</a></li>
    <li><a href="#">Menu Item1</a></li>
    <li><a href="#">Menu Item1</a></li>
    <li><a href="#">Menu Item1</a></li>
    <li><a href="#">Menu Item1</a></li>
    </ul>
    </nav>
    <div id="wrapper">
    <!--begin main content-->
    <img class="banner" src="http://placehold.it/1056x100/198EBA/FFFFFF&text=Banner.jpg" alt="banner" />
    <article> <h3>Article</h3>
    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris vitae libero lacus, vel hendrerit nisi!  Maecenas quis velit nisl, volutpat viverra felis. Vestibulum luctus mauris sed sem dapibus luctus.  Pellentesque aliquet aliquet ligula, et sagittis justo auctor varius. Quisque varius scelerisque nunc eget rhoncus.  Aenean tristique enim ut ante dignissim. </p>
    <figure> <img src="http://placehold.it/500x325" alt="placeholder">
    <figcaption>Figure 2 Caption</figcaption>
    </figure>
    </article>
    <!--begin right sidebar-->
    <aside> <h3>Aside</h3>
    <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris vitae libero lacus, vel hendrerit nisi!  Maecenas quis velit nisl, volutpat viverra felis. Vestibulum luctus mauris sed sem dapibus luctus. </p>
    <hr>
    <p>Pellentesque aliquet aliquet ligula, et sagittis justo auctor varius. Quisque varius scelerisque nunc eget rhoncus.  Aenean tristique enim ut ante dignissim. </p>
    <hr>
    <p>Pellentesque aliquet aliquet ligula, et sagittis justo auctor varius. Quisque varius scelerisque nunc eget rhoncus.  Aenean tristique enim ut ante dignissim. </p>
    </aside>
    <!--end wrapper--></div>
    <!--begin footer-->
    <footer> <small>© 2014 Your Site Name. All rights reserved</small> </footer>
    </body>
    </html>
    Nancy O.

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