Template file provided by hook_theme_registry_alter() could not be override in theme layer.

theme_breadcrumb is provide by theme.inc, in module breadcrumb2(http://drupal.org/project/breadcrumb2 ), I change it to a template file by using hook_theme_registry_alter. In a project, I copy breacrumb.tpl.php to theme directory, try to override it in theme layer, after i clear the cache again and again, it still does not work. Here is my code:

/**
 * Implements hook_theme_registry_alter().
 */
function breadcrumb2_theme_registry_alter(&$theme_registry) {
  if (isset($theme_registry['breadcrumb'])) {
    $path = drupal_get_path('module', 'breadcrumb2');
    $theme_registry['breadcrumb']['path'] = $path;
    $theme_registry['breadcrumb']['template'] = 'breadcrumb';
    $theme_registry['breadcrumb']['function'] = NULL;
  }
}

Although it was fixed in latest version of breadcrumb2 module, I still think that this is bug of drupal core. Other developers have the same experience when they implement hook_theme_registry_alter, Most of them do not know how to fix it.

Sollutions:
(1),fix it in drupal core, using following code instead:

function _theme_build_registry($theme, $base_theme, $theme_engine) {
  $cache = array();
  // First, process the theme hooks advertised by modules. This will
  // serve as the basic registry. Since the list of enabled modules is the same
  // regardless of the theme used, this is cached in its own entry to save
  // building it for every theme.
  if ($cached = cache_get('theme_registry:build:modules')) {
    $cache = $cached->data;
  }
  else {
    foreach (module_implements('theme') as $module) {
      _theme_process_registry($cache, $module, 'module', $module, drupal_get_path('module', $module));
    }
    // Only cache this registry if all modules are loaded.
    if (module_load_all(NULL)) {
      cache_set('theme_registry:build:modules', $cache);
    }
  }

  // Let modules alter the registry.
  drupal_alter('theme_registry', $cache);

  // Process each base theme.
  foreach ($base_theme as $base) {
    // If the base theme uses a theme engine, process its hooks.
    $base_path = dirname($base->filename);
    if ($theme_engine) {
      _theme_process_registry($cache, $theme_engine, 'base_theme_engine', $base->name, $base_path);
    }
    _theme_process_registry($cache, $base->name, 'base_theme', $base->name, $base_path);
  }

  // And then the same thing, but for the theme.
  if ($theme_engine) {
    _theme_process_registry($cache, $theme_engine, 'theme_engine', $theme->name, dirname($theme->filename));
  }

  // Finally, hooks provided by the theme itself.
  _theme_process_registry($cache, $theme->name, 'theme', $theme->name, dirname($theme->filename));

  // Optimize the registry to not have empty arrays for functions.
  foreach ($cache as $hook => $info) {
    foreach (array('preprocess functions', 'process functions') as $phase) {
      if (empty($info[$phase])) {
        unset($cache[$hook][$phase]);
      }
    }
  }
  return $cache;
}

(2), Dirty way to fix it in breadcrumb2:

/**
 * Implements hook_theme_registry_alter().
 */
function breadcrumb2_theme_registry_alter(&$theme_registry) {
  if (isset($theme_registry['breadcrumb'])) {
    $path = drupal_get_path('module', 'breadcrumb2');
    $theme_registry['breadcrumb']['path'] = $path;
    $theme_registry['breadcrumb']['template'] = 'breadcrumb';
    $theme_registry['breadcrumb']['function'] = NULL;
  }
  global $theme;
  $themes = list_themes();
  $theme_obj = $themes[$theme];
   _theme_process_registry($theme_registry, 'phptemplate', 'theme_engine', $theme_obj->name, dirname($theme_obj->filename));
}

I have to recall _theme_process_registry by myself.