the box() method in PGraphics3 has 4 normals with the wrong sign.

Correct vertex/normal chunk should read:

beginShape(QUADS);

// front
normal(0, 0, -1);
vertex(x1, y1, z1);
vertex(x2, y1, z1);
vertex(x2, y2, z1);
vertex(x1, y2, z1);

// right
normal(1, 0, 0);
vertex(x2, y1, z1);
vertex(x2, y1, z2);
vertex(x2, y2, z2);
vertex(x2, y2, z1);

// back
normal(0, 0, 1);
vertex(x2, y1, z2);
vertex(x1, y1, z2);
vertex(x1, y2, z2);
vertex(x2, y2, z2);

// left
normal(-1, 0, 0);
vertex(x1, y1, z2);
vertex(x1, y1, z1);
vertex(x1, y2, z1);
vertex(x1, y2, z2);

// top
normal(0, -1, 0);
vertex(x1, y1, z2);
vertex(x2, y1, z2);
vertex(x2, y1, z1);
vertex(x1, y1, z1);

// bottom
normal(0, 1, 0);
vertex(x1, y2, z1);
vertex(x2, y2, z1);
vertex(x2, y2, z2);
vertex(x1, y2, z2);

endShape();

hm, i don't think so.. you're sure you have the right coordinate system?
http://processing.org/reference/environment/index.html#Coordinates

I was fiddling with the OpenGL system, and changed the glScalef from 1,-1,1
to 1,1,1 and that needed the change, seems counter intuitive that normals
need to change, but I've read there can be issues with normals and scale.

This can probably be closed.