This is unusual behaviour. I would recommend checking the following:
- Check that Free Object is unchecked.
- If you're using clipping splines, check that the RailClone object is still oriented so that it flat on the spline area. If could be that the spline got rotated but the RailClone object did not
- Reselect all the base splines, sometimes this forces an update and sorts things out.
- The RailClone Objects can't be instanced (they use different base splines) If this is the case make them unique and re-assign the correct splines.
If none of that helps, would it be possible to send me the problematic objects and their base splines? Please send them to firstname.lastname@example.org if you'd rather not share them publicly.