OK, so, if I carve out the handrail using boolean subtraction it comes out right. If I extrude it from a flat shape it comes out back to front.

In blender they look similar but SH3D interprets them differently.

I tried to diff the OBJ files but there were too many differences. I can export just the handrails in each case and compare them. Don't know if the devs would find this useful for future reference?