I suspect this is due to the alignment of the pivots and the RailClone object. There are a couple of important things to remember with creating vertical clipping areas:
1. The source geometry should be aligned with its local XY axis. I often rotate the geometry to match the XY axes of world space and then reset the XForms to be certain of this.
2. When using Clipping to set the size of the area RailClone builds the 2d array on its local XY axis. This means that if your clipping spline is vertical you'll need to rotate the RailClone object to align with the clipping spline. You don't however need to worry about the axis orientation of the spline itself. Please see the image below and the attached file for an illustration. If you'd like to know more about clipping spines, check out this chapter
in our Next Steps with RailClone guide.
I hope that helps.