I've been able o resolve the issue, but it took some doing. I'm not sure where the change might have occurred. ( I updated my corona version along with forestpack and railclone to all the latest versions) The proxy house that I was using had the base transforms flipped in a weird way, which may have been like that from the beginning, but possibly corona proxy and/or forestpack changed how it was interpreting the transform in laying it out across the spline.
Even when I turned the objects back into meshes and tried to reset the transform it kept flipping back. I had to create a box, attach the mesh to it and then delete the box for it to maintain the right transform. I'm not sure why or how this was happening, but maybe the object was corrupt.