Next texture I made by hand in Photoshop. I aligned it in Blender (using Jazz). But now when I upload it to SL, the texture does not fit the object anymore.

I had made a goblet with glass on a metal leg. In the glas part the same problem showed up as with two transparent object behind each other. Thought the sculpt is just a single prim object, SL seems not to be able do show the frontsite first and the the backsite second… at least not all the time.

You can’t bake refraction into a texture because it’s an effect that depends on a static camera point of view and environment. When you bake textures, a virtual camera moves around the mesh and takes pixel snapshots along the surface normals. This barely works for specular reflection but totally fails for any kind of raytracing or environment mapping.

I guess the best way to bring such a glass into SL is to extend the area covered by specular highlights, e.g. by reducing specularity hardness or adding more lamps, so that the texture blends between semi-opaque and almost transparent in a way that resembles reflections on real glass.

You say you are using ray transparency, but raytraced transparency does not produce (alpha-)transparent textures when baked.

Maybe you are trying to work around that in your node setup, and that’s what is causing the artifacts. It’s difficult to tell without looking at the nodes. When I bake transparent textures with Z-transparency, I never see artifacts like these (unless there are flipped normals or zero-sized faces, but you already ruled these out when we talked yesterday).