this is due to some revisions in the way that RailClone tools works. The changes were made to allow us to respect material ID and UVW XForm randomisation, but they do cause objects that use these features to be collapsed to a single mesh. To prevent this you'll need to open the style and remove or disable the UVW Xform and Material nodes.
We're looking into adding more options to RailClone tools so that you can choose to ignore those nodes and restore full instancing.
I hope that helps, please let me know if you have any further questions.