Secondary menu keep showing

Removing the secondary menu is working correctly for me locally. How are you enabling and disabling the secondary menu? You should be able to toggle it on the theme's configuration page. If that is not working for you please let us know. Attached is a screenshot showing the correct toggle for reference.

Going to assume fixed with no report back

I have the same issue. I have tried turning the secondary links off as per the image above for 'global settings', 'acquia prosper', 'fusion core' and 'fusion starter' and they are still showing.
I am using the 6.x-1.0-beta3 version of fusion and acquia prosper.

Have you updated to the latest version of Fusion and Acquia Prosper? Even though there is no if/then statement for the secondary menu it won't print if the checkbox is disabled for Acquia Prosper's secondary menu. Not sure why it's not working on your server though as every other place I've tried it it works correctly.

Me too, I'm in 6.x-1.0-beta4 and I've put the secondary menus at the postcript area where I like them, but cannot turn them off at header top even by disabling in all themes and flushing cache. They just won't go away? I have no search box enabled and nothing else in those areas.

been using drupal for 2 days now and php newbee (please let me know if im doin this wrong)
cause so far it worked for me

this was not the secondary menu, its actually a duplicate left in the header.

solution
in ../themes/acquia_prosper/page.tpl.php

<!-- primary-menu row: width = grid_width -->
      <div id="header-primary-menu-wrapper" class="header-primary-menu-wrapper full-width">
        <div id="header-primary-menu" class="header-primary-menu row <?php print $grid_width; ?>">
          <div id="header-primary-menu-inner" class="header-primary-menu-inner inner clearfix">
         <!--?php print theme('grid_block', $primary_links_tree, 'primary-menu'); ?-->    //comment this line out
          </div><!-- /header-primary-menu-inner -->
        </div><!-- /header-primary-menu -->
      </div><!-- /header-primary-menu-wrapper -->

      <!-- preface-top row: width = grid_width --> 

I'm really not sure exactly what's going on here. We can't replicate this. The theme() functions already check if it's there or not, so you don't need a conditional around them.