Transparent textures on a model make parts inside it invisible.

Probably relates to MC-50129, but I think it might be a different issue.

When I was making a model for the ender pearl and eye, the transparent outer part of the model made the inner parts of the model invisible.

Again, this probably relates to MC-50129 but I'm not entirely sure.

EDIT - Similar things to MC-50129 happen in the achievement menu, as the inside of the ender eye renders outside the outer cube.