If you are instancing RailClone objects that use base spline, please remember that the same base will be applied to all instances. Changing one will change them all. This will result in the RailClone objects appearing on top of one another which may be why they look like they're disappearing. If you want to retain the shape of the base spline but move the objects independently of it, you can turn on Free Objects in the Style rollout. This allows you to move the geometry away from the path and may be helpful for instancing.
I hope that helps, please let me know if you have any further questions.