RailClone ignore thes splines pivot but uses it's own local axis to determine the direction of spline clipping so in this case you could rotate the RailClone object around its Z axis until it matches the orientation of the spline. You'll then probably need to reselect the path to update the geometry but the spline will now be clipping correctly.
Alternatively, since in this case you are removing the full height of the style, it may make more sense to draw a cliping spline in the top view and change the projection mode to Z
. This will avoid the need to reorientate the RC object.
I hope that helps, please let me know if you have further questions.