It seems the RailClone object was created in the XZ plane, so when the spline is rotated 90º the direction as seen from RC is a vector with X:0, Y:0.
That causes an indetermination to get the Z axis, which is computed as the perpendicular of this vector.
How to fix it:
1) Select the spline in Base Objects and click "Realign". That will align RC with the local axis of the spline (XY).
2) In the Generator properties, set X Rotation = 90º.
I suggest this procedure to create rotated arrays, because several computations in RC are done considering that the object is aligned on the XY plane.