RailClone holds the references to segments in two ways:
1) Directly to the source object if it exists in the scene. In this case, you can see the name of the object in the segment node (in the style editor)
2) If the source object is deleted or the style is imported from the library, the geometry is stored internally. The name of the object is shown as "--embedded--" in the segment's properties.
But in both cases, RailClone tries to share these references when possible, to not duplicate geometries. For example, when a style is assigned from the Library to multiple objects, or when using any of the "Copy Style" procedures.
So, this problem is strange, because theorically all your objects should share the same references. I've done a quick test here, and everything works as intended.
Please, run this Maxscript command and tell us the result. You must replace "RailClone001" and "RailClone002" with the name of two RC objects:
$RailClone001.sobjref == $RailClone002.sobjref
It will return "true" if both share the same reference (for the first segment), and false if not.