I'm not sure exactly where this bug lies, but pinning it on difference seems to
be the most logical thing.  Here's some sample code:

#version 3.7;
#include "colors.inc"

global_settings {
  max_trace_level 256
  ambient_light White
  assumed_gamma 1.0
}

camera {
  location <0,10,0>
  look_at <0,0,0>
}

light_source {
  <1000,1000,0>
  color White
}

plane {
  y, -10
  pigment { hexagon Green, White }
}

box {
  <-0.9999, -0.9999, -0.9999>, <0.9999, 0.9999, 0.9999>
  pigment { checker Violet, Yellow }
}

difference {
  box {
<-1.0000149999,-1.0000149999,-1.0000149999>,<1.0000149999,1.0000149999,1.0000149999>
}
  box { <-1, -1 ,-1>,<1,1,1> }
  pigment {
    transmit 0
  }
  finish {
    ambient 0
    diffuse 0
    conserve_energy
    reflection {
      1
      fresnel on
    }
    specular 0
    roughness 0.001
  }
  interior {
    ior 1/sqrt(2)
  }
}

difference {
  box { <-1.00003,-1.00003,-1.00003>,<1.00003,1.00003,1.00003> }
  box { <-1.000015, -1.000015 ,-1.000015>,<1.000015,1.000015,1.000015> }
  pigment {
    transmit 1
  }
  finish {
    ambient 0
    diffuse 0
    conserve_energy
    reflection {
      0
      fresnel on
    }
    specular 0
    roughness 0.001
  }
  interior {
    ior 1
  }
}

If you render the above, you should see a black square with a backdrop of
hexagons (the plane).  However, you see a checkered square with a backdrop of
hexagons.  If you comment out the second difference (the one with the ior of 1),
you will see what you are supposed to see.  There should, however, be no
difference since an ior of 1 corresponds to air!  When I rendered this with
POV-Ray 3.6, I saw a black square which confirms that this a bug that has crept
in during the development of 3.7.

- Chaanakya

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