Secondary Links option available but they are not supported

This theme is designed to display only primary link lines and you will see the result like you did if you choose to display secondary link too. Sorry but this is how this theme is designed.

Will this be changed in the future?

A solution for the secondary links problem coul be building a block with them in an place it in the bottom of the main content.

mmm, for this purpose I would like to know how to build a block that doesnt display the header colored bar

Or placing them underneath the search box looks nice. Using the dark color from the color set it changes with color module.

To do this move <?php if (isset($secondary_links)) { ?><?php print theme('links', $secondary_links, array('class' =>'links', 'id' => 'subnavlist')) ?><?php } ?>

to just under print $search_box like this:

    <td id="site_search">
      <?php print $search_box ?>
      <?php if (isset($secondary_links)) { ?><?php print theme('links', $secondary_links, array('class' =>'links', 'id' => 'subnavlist')) ?><?php } ?>
  </td>

and in style.css change:

#subnavlist {
  padding: 0.5em 1.2em 0.4em 0;
  font-size: 0.8em;
  color: #aaaaaa;
}
#subnavlist a {
  font-weight: bold;
  color: #aaaaaa;
}

to:

#subnavlist {
  padding: 0.5em 1.2em 0.4em 0;
  font-size: 0.8em;
  color: #b21f88;
}
#subnavlist a {
  font-weight: bold;
  color: #b21f88;
}

I propose we get rid of secondary links entirely.

Main reasons is the theme does not support them well and the current implementation is rather confusing for new users. Anyone who knows what they are doing can implement secondary links anywhere they want such as level02's suggestion.

As a compromise we could just leave the secondary code block in page.tpl.php and comment out support for them in pixture.info