Thanks for getting in touch. If you are using the clipping path to automatically set the XY dimensions of a 2d Array, RailClone uses the spline projected on the RailClone object's local Z axis. The easiest way to get this to work therefore is to create the spline and RailClone object so that their local Z axis align, either by creating them both in the same orthogonal viewport or by creating on the xy axis in perspective and later rotating both into place. You can also use the realign button from the base objects rollout to automatically match the RailClone object to the base spline's rotation and position.
Hope that helps,