According to wiktionary the word is said to derive from Latin 'denigratus,' to blacken; or asperse, defame. There's also Latin 'denigratio,' said to mean blackening.
Yet doesn't the prefix 'de' mean to take away from?
So wouldn't denigrare/denigro mean 'to remove the blackness of/from'?
I can't think of any other examples that would be consistent with this. Someone might say flammable / inflammable, but that at least makes some sense. Flammable = able to become flames. Inflammable = able to become inflamed/burned. That wouldn't really apply here.
Any help/thoughts appreciated.