ShadowBox not working on Homepage

Hello everyone,

I recently installed the Shadowbox JS plugin. it works fine for normal pictures in posts. All i do is put the youtube link in the “link url” area such as http://www.youtube.com/v/xxxxxxxxxxx

I want to do the same for the featured image on the homepage but the link doesn’t stay. When you click it just goes to the post. Anyone know how to fix this?

Also, for just regular images in the post that open up in shadowbox to videos, the video has these random black boxes across it. anyone know how to get rid of those? thanks!