Sounds like Im the only one who uses .x3db
In my experience, colour models for FCS are very finicky, ie getting the texture to upload with the model correctly to shapeways can be a battle.
Theres various things that can go wrong, but I can suggest a few things - first make sure the texture is mapped to every face on the model, in the past even having one face which hasnt got the texture applied will cause shapeways to reject the texture or be unable to find it.
Make sure your applying the exact same texture to the model which your also putting in the .zip and that the name is exactly the same.
I use Blender and, for example, if you open a 2nd version of a image in the program it will be named texture.001.jpg, even though the source image is named texture.jpg, exporting that model with texture.001.jpg applied to it and putting it in a .zip with texture.jpg will result in a non-textured model on shapeways.
As for the FCS material not appearing, try going into the edit page for the model on shapeways and re-enable the materia, FCS could just be disabled as a material option there, its happened to me before.
I dont know how this would work in other programs, or with other model formats for that matter, but those are some of the issues I've encountered personally.
*Edit* Whoops, didnt realise how old this thread was...