No highlighting with 7.x-2.0-alpha6

What do you mean by "emptying chili_highlighter.js"?

I didn't have to empty the "chili_hilighter.js" file; I changed the weight of the loaded JavaScript files, and it worked.

I changed the code of chili_highlighter_init() to the following one:

function chili_highlighter_init() {
  if ($plugin_path = chili_highlighter_plugin_path()) {
    $external = url_is_external($plugin_path);
    $module_path = drupal_get_path('module', 'chili_highlighter');
    $recipe_folder = $external ? $module_path . '/js/' : $plugin_path . '/';

    drupal_add_js(
      array(
        'chiliHighlighter' => array(
          'recipeFolder' => base_path() . $recipe_folder,
          'selector' => '.chili-highlighter',
        )
      ),
      'setting'
    );

    // Third-party modules can change the plugin path to an external link.
    if ($external) {
      drupal_add_js(
        $plugin_path,
        array('type' => 'external', 'group' => JS_LIBRARY, 'weight' => 0)
      );
    }
    else {
      drupal_add_js(
        $plugin_path . '/jquery.chili.js',
        array('type' => 'file', 'group' => JS_LIBRARY, 'weight' => 0)
      );
    }

    drupal_add_js(
      $plugin_path . '/recipes.js',
      array('type' => 'file', 'group' => JS_LIBRARY, 'weight' => 1)
    );

    drupal_add_js(
      $module_path . '/js/chili_highlighter.js',
      array('type' => 'file', 'group' => JS_LIBRARY, 'weight' => 2)
    );
  }
}

I also changed the content of the "chili_hilighter.js" file to the following one:

(function($) {

ChiliBook.lineNumbers = false;

Drupal.behaviors.chiliHighlighter = {
  attach: function(context, settings) {
    $(settings.chiliHighlighter.selector, context).once('chilihighlighter', function() {
      $(this).chili();
    });
  }
};

})(jQuery);

I still have to resolve a bug, which doesn't allows to select a different tag to highlight. Monday I will change the code to resolve that bug too, and I will commit the code to create a new official release.
After that I will back-port the code for Drupal 6.

Thank you for your report, and help in fixing this issue.

add more info on how to fix

I have created a new official release.

Use the recipes attached in http://drupal.org/node/1270364.
The version associated with the filename is the minimum module version that uses those recipes. Use the file for the version that is closer to the version of the module you are using; for example, if you find two archives, recipes-7.x-2.0-alpha7.zip and recipes-7.x-2.0-alpha9.zip and you are using version 7.x-2.0-alpha11 of the module, then use the file recipes-7.x-2.0-alpha9.zip.