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Let me ask this in another way, why would you not use two different colors as one, if they look identical to you?

Why would you separately put two "different" colors of paint on your pad, when as far as you can tell they are identical?

I can understand mixing them, or using first one then the other (after you run out of one) - but shading the image partly with one color and parts with another?

The only conclusion is that they were not identical to him, and this software is not correctly showing us what he saw.

Simple: You mix the colors one way, paint for a while, go off to some other part, mix the first color again, and paint again. If you can't tell the differences between two colors, it's easy to come up with two similar/'identical' colors that are really quite different to someone with a different color perception.

While this article doesn't remotely prove that this is what's happened, it seems like a possibility to me.

The effect where colors with different spectral power distributions matches under certain conditions due to the observer or the light source, is called metamerism.

http://en.wikipedia.org/wiki/Metamerism_%28color%29

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