Oddly the Lightbox Repeater doesn't have Hierarchy support, so i'm curious how it's properly handling hierarchy. Makes me almost wonder if you have a nested repeater in the transformation and that's where you are missing the order by.
Either way, just a heads up that the Repeater with Lightbox was removed in version 9, the better way to do this is to use the Universal Viewer / Hierarchy Viewer (making sure to check to Load Hierarchy Data), and create your Hierarchy Transformation to render things properly. Then the NodeLevel, NodeOrder will work properly.
Can you copy what you have for the LightboxVideosYoutube transformation?