The RailClone plug-in builds the array based on its local coordinates - as in your case it's not perfectly vertical, I would suggest you to recreate the RC object using a Helper - Grid (or quickly by using the AutoGrid option). To perform slicing correctly the Clipping Area option should be set to For No-Slice - Slice and used Segment ("GlazingB") should have the Deform - Slice option disabled. We'll investigate why it's in this specific case needed.
Attaching modified scene. Hope you'll find it useful.