When creating a custom model, adding stained glass textures or any transparent textures are no longer see through in the actual game. Instead, they are solid. If you put the model on something that already has transparency like stained glass, it will work as it use to. (The textures seem to clash a little more than before though)

While as mentioned before that it does work with the right item, it doesn't work with all of them like it use to so I assume this is a bug.