Drupal's default jQuery doesn't get called when the CDN and jQuery options in the theme settings are left at their default values.
Here's the portion of template.php causing the issue:
// If a CDN is not selected, but an updated version still wants to be used.
$js['misc/jquery.js']['data'] = "$path_to_theme/js/jquery-$version.min.js";
It doesn't check if the default jQuery is in play and automatically looks for the file in Aurora's folder.