Primary and Secondary Links Appear In the Header Block and Covered Up by the Logo

I am not sure this is a bug because I am not sure whether this was intended. The Secondary links are not just appearing where they should in the block to the left of the content but also in the header where the logo and site name are. These links are not positioned to clear the logo and title so the first few links are partially covered up by the logo. I do not want these links there. The problem is in the lines 39 through 44 of the file "page.tpl.php" where both the Primary and Secondary links are printed in the header block. Copied here are lines 11 through 50:

    <div id="header">
      <div class="r1"></div><div class="r2"></div><div class="r3"></div><div class="r4"></div><div class="r5"></div>
      <div class="content">
        <!-- Header -->
        <div id="logo-floater">
        <?php
          // Prepare header
          $site_fields = array();
          if ($site_name) {
            $site_fields[] = check_plain($site_name);
          }
          if ($site_slogan) {
            $site_fields[] = check_plain($site_slogan);
          }
          $site_title = implode(' ', $site_fields);
          $site_fields[0] = '<span>'. $site_fields[0] .'</span>';
          $site_html = implode(' ', $site_fields);

          if ($logo || $site_title) {
            print '<h1><a href="'. check_url($base_path) .'" title="'. $site_title .'">';
            if ($logo) {
              print '<img src="'. check_url($logo) .'" alt="'. $site_title .'" id="logo" />';
            }
            print $site_html .'</a></h1>';
          }
        ?>
        </div>

        <?php if (isset($primary_links)) : ?>
          <?php print theme('links', $primary_links, array('class' => 'links primary-links')) ?>
        <?php endif; ?>
        <?php if (isset($secondary_links)) : ?>
          <?php print theme('links', $secondary_links, array('class' => 'links secondary-links')) ?>
        <?php endif; ?>

        <?php print $header ?>
      </div>
      <div class="r5"></div><div class="r4"></div><div class="r3"></div><div class="r2"></div><div class="r1"></div>
    </div>

Look under the

if (isset($primary_links)) :

line. My fix removes the redundant Secondary links from the header, and moves the primary links to its own block just under the header. My code fix:

    <div id="header">
      <div class="r1"></div><div class="r2"></div><div class="r3"></div><div class="r4"></div><div class="r5"></div>
      <div class="content">
        <!-- Header -->
        <div id="logo-floater">
        <?php
          // Prepare header
          $site_fields = array();
          if ($site_name) {
            $site_fields[] = check_plain($site_name);
          }
          if ($site_slogan) {
            $site_fields[] = check_plain($site_slogan);
          }
          $site_title = implode(' ', $site_fields);
          $site_fields[0] = '<span>'. $site_fields[0] .'</span>';
          $site_html = implode(' ', $site_fields);

          if ($logo || $site_title) {
            print '<h1><a href="'. check_url($base_path) .'" title="'. $site_title .'">';
            if ($logo) {
              print '<img src="'. check_url($logo) .'" alt="'. $site_title .'" id="logo" />';
            }
            print $site_html .'</a></h1>';
          }
        ?>
        </div>
        <?php print $header ?>
      </div>        
      <div class="r5"></div><div class="r4"></div><div class="r3"></div><div class="r2"></div><div class="r1"></div>
      <?php if (isset($primary_links) && !empty($primary_links)) : ?>
         <div class="r1"></div><div class="r2"></div><div class="r3"></div><div class="r4"></div><div class="r5"></div>
         <div class="content">
         <?php print theme('links', $primary_links, array('class' => 'links primary-links')); ?>
         </div>
         <div class="r5"></div><div class="r4"></div><div class="r3"></div><div class="r2"></div><div class="r1"></div>
       <?php endif; ?>
     </div>