In Railclone you are responsible of create a material and apply it to the final railclone object. The segment's material is not used in any part of the construction. The only place where rail clone material it is changed automatically, is when you import styles from the library, that it is not this case.
If there is different materials per element, you need to create your own multi sub material, assigning a different material Id to each element and applying it to the whole rail clone object.