Thanks for your question. In order for RailClone to cap geometry, it uses a native 3ds Max boolean function. As with any boolean, a watertight mesh is required for it to work correctly. Since the mesh you are using is open on the bottom it won't cap, the solution, therefore, is to create closed meshes if you intend to use this feature. Once you've made that change, you may still find the occasional gap, again, unfortunately this is a limitation of Max's boolean algorithms, although I have found that increasing the Curve Steps property in RailClone's Style rollout can improve it a little. Another trick is to convert the source geometry to an editable mesh and then make all edges visible, This seems to significantly improve the boolean results.
I hope that helps,