In that scene I was able to fix the issue with a couple of steps.
1 - Change the spline's pivot so that it is aligned to the world axis.
2 - RailClone 3 has extra settings for clipping splines. One of these is called Hierachy Checking and for splines objects with multiple splines, it enables you to determine when a new array is created. The options are:
None Each spline generates a new array
Complete All splines are used to calculate clipping areas. If one spline is inside another or overlaps it is used to either clip the array or add a new one. (This is the RC2 behaviour)
Material ID This allows you to group together splines into material IDs - Each ID should creates it's own array. This works well for situations like your file where you have multiple overlapping splines, but each one is contributing to a different facade. In this case, give each group of splines a different ID and it should work as expected.
I hope that helps, please let me know if you have any further questions.