Ok, i see the problem: RailClone computes the banking angle using the previous angles along the spline, in order to create a smooth transition. Unfortunately this method generates a "break" in the start/end point of closed splines.
It seems this is a common issue, because the Sweep modifier has the same problem (see attached screenshot). Ideally, would be necessary to include a "banking" editor, so the user can adjust the angles in each case. This feature was already in our RC wishlist, although it is not simple to implement.
Unfortunately, the only solution in this case would be to edit the RC mesh, rotating manually the final pieces.