Hi, once you add a scene, this is added only in the slide show, that is where all scenes and stills are loaded. If you have set another movie as default in the preview and publish window, the scenes added will not show up. Or you edit your default movie, copying the scene in the copy of the slide show or just to test, change the default movie under "Publish settings" "HTML" tab. Finally to get the secene added also in the thumbnail scene list, you have to go to main window, select the thumnails and under properties click list values and there you will see the scene list where you can choose which you want to be shown.
If it is not clear, please let me know and I will keep trying