Another option is to change the Hierarchy checking mode.
As far as I recall the presets are set up using "Complete" hierarchy checking mode which attempts to work out which splines belong to which part of a wall, but when walls are opposite one another it can be a challenge. Instead there is a Material ID mode, which uses IDs assigned to the spline to tell RailClone which splines belong together. In situations like the ones in your screenshots, it'll work much better. To enable it.
- Open the Style Editor.
- Select the Cladding Macro
- In its properties, change Hierarchy mode to 2
- Group splines from the same wall together by assigning them the same material ID.
Disable the instancing engine in the Display rollout to get the Material feature to work. Unfortunately this is a limitation with Corona, but disabling instancing should fix it.
I hope that helps,