Without more specific information I would say that this is a PBR texture issue. You stated that you tried non-PBR textures but does the track use PBR for its ballast? The problem seems to occur when the two, PBR and non-PBR, meet.
What is your Shader Quality setting in the Trainz Settings Performance tab? If it is "Ultra" change it to "Standard" to see if that makes a difference.