Menutrails breaks breadcrumbs

I can confirm this. It also breaks book breadcrumbs. This makes it rather unusable - conflicting with two major core modules like this.

Surely if no trail is set for a particular content type or taxonomy, Menu Trails should leave the breadcrumbs entirely alone?

Confirmed. If I enable it on a page that already had a "Home" breadcrumb, I get a double-Home breadcrumb: "Home -> "Home". See example at http://www.bebr.ufl.edu/content/lee-economic-output-nosedives.

Yes a i have the same problem
I modify menutrails_get_breadcrumbs function like this

function menutrails_get_breadcrumbs() {
  $item = menu_get_item();
  if (!$menu) {
    // give first priority to the selected menu
    $menu = variable_get('menutrails_menu', FALSE);
    if (!$menu) {
      $menu = db_result(db_query("SELECT menu_name FROM {menu_links} WHERE link_path = '%s' AND module = 'menu'", $item['href']));
    }
  }
  $tree = menu_tree_page_data($menu);
  if(!drupal_is_front_page()){
    $crumbs = array(l(t('Home'), '<front>'));
  }
  _menutrails_recurse_crumbs($tree, $item, $crumbs);
  return $crumbs;
}

Yokan: You're looking at a 5.x issue, that function is in the 6.x version of the module.

Sorry, Menu Trails for Drupal 5 is not actively developed/maintained anymore. Only issues containing patches may still be considered. Feel free to re-open this issue if you want to provide a patch.