Thank you for writing in, lightbox shortcode still works as always. Please test for a plugin conflict. You can do this by deactivating all third-party plugins, and see if the problem remains. If it's fixed, you'll know a plugin caused the problem, and you can narrow down which one by reactivating them one at a time.
Not only plugins but also custom scripts that you might have added to your site.
Also please ensure you are fully up to date and it is in a compatible version. WordPress, Theme, and Cornerstone (Version Compatibility).