The problem you are having is not a JOGL, or even OpenGL problem. It is a general 3D rendering issue. Here’s a blurb from my 3D engine chapter that will explain it better.
Render Order
It turns out that simply rendering in whatever order was in the scene list will probaby not work for most scenes. The reason is that transparent objects will probably not end up rendering correctly. Transparency is not automatically correct in modern 3D hardware but instead requires significant effort to be correctly implemented in a 3D engine.
Transparent objects need to be rendered with the proper OpenGL blending function after all other opaque objects are rendered before them to actually look transparent. Additional, within that transparent object render pass the transaprent objects must also be rendered farthest to nearest from the camera’s perspective. To be totally correct they have be rendered far to near on a face by face basis, and if any geometry intersecting, the intersecting faces would have to be split and sorted. Whew!
Totally correct scene transparency is often incredibly expensive to compute, especially for dynamic transparent geometry such as particle systems, so real-time 3D engines do the best they can by supporting depth sorted transparent objects, and rendering them after all the opaque objects.
Also if you are transforming your geoemtry, then you will be use that to get the objects “location” or z-depth for the sorting.
