When you look at a transparent object what you mainly see is a distorted image of the background that changes from one direction to another, not the object itself.
Although Foto 3D can capture the geometry of the object if the masks are accurate enough, the surface texture generated from lots of images tends to be blurred and confused.
This is something Foto 3D shares with all 3D modeling packages. Advanced users can edit the textures to improve the results but the model may still look lifeless compared to the original unless the rendering can show the effects of transparency.
Although highly reflective objects similarly reflect the background, the results tend to be much more acceptable, and if an environment map is added so that the reflections change with the direction the object is viewed from, then the objects will look convincingly reflective.