Radiation damage? Compare http://en.wikipedia.org/wiki/Smoky_quartz

Try annealing the sample. If the color goes away, it is probably radiation damage because such damage is healed out upon annealing.

I shall check. That is an interesting possibility.

there is some reasons: in addition to radiation damage, some cations (Fe+3 etc.) and micro solid inclusions such as clay minerals or organic material can be the culprit...

Annealed the sample at 350C for 48 hours, the white areas got whiter, but the black and brown areas saw no change. What would carbon do in a salt crystal matrix? I can understand it turning the top black if an over-heated hydrocarbon (charring) was in contact with the surface, but I still can't explain the brown layer.

The material came from a pipeline deposit that was clogging a pumping system. I've had the material sitting out in the open for almost a year and up to about 3 months ago it was still leaching an oil due to capillary action. I'll run it again on XRD to see if something else shows up. I have a very clear carbon line now visible on the very surface of the material on top of the thicker black layer.

The presence of microquantities of different compounds, that could be of different halides and sulfates of cations could change the color of the NaCl, but the method you are using is not good enough for the small quantities you have in your sample, you can have the signs of the compound that produces the change in color but the signs are covered by the big picks produced by NaCl

I recommend Antonio's answer

Best Regards