Hi, thanks for reporting the problem. This issue is caused by the spline adaptation over the surface. The bug is already fixed for RailClone 3.
Until update is released, as workaround you would conform the spline using our Glue
plugin, and use it in RC.
Please note that Glue doesn't preserve IDs either, so you need to set them again once spline is conformed.
I hope that helps. Apologies for any inconvenience.