Perhaps the missing shaders are on "global" rather than local coordinates? When the object is moved, then the shader changes (?) I am just grasping at a possibility, as I have never had a shader malfunction either.
Do all the shaders have unique names? Do all the material zones CALL for unique names? If one of these is the culprit, then Carrara would open the shader, but apply a different one first. (Still grasping.)