These issues are caused by two separate issues that relate to the way that RailClone uses surfaces.
In the areas marked 1, RailClone is deforming the geometry because it slightly extends beyond the boundaries of the surface. The RailClone object must be completely inside the surface boundaries to work correctly. In fact it works best if the surface extends slightly further beyond the RailClone geometry. For some scenarios such as this, it may be necessary to create a slightly larger, non-renderable surface to use with RailClone.
The area marked 2 is caused because of the way RailClone projects geometry. It is pushed along the Local Z axis until it encounters geometry, however this is not dependent on the original Z location of the spline, it will always use the top most polygons. In this scenario you would need to create two RC objects and split the roofs into two poly objects for use as surfaces, one for each level.
I hope that helps, please let me know if you have further feedback.