Soooo I've started a tumblr. Not sure where that'll take my bleak, depressive self to, but 'aight.
Some of Gwyn’s Silver Knights left with him to combat the demons that were created when the Witch attempted to recreate the Fire. They came back with blackened armor. It was clear to Gwyn through his failure that the era was coming to an end either way, so he took some of the knights with him to rekindle the First Flame. Whether those were also Silver Knights that became black as well, who knows. But that’s why some are specked all over the place.
Some of the reason why a lot of things in DaS1 may not make a lot of sense (what the hell are demons? why are miracles and sorceries separate? if the gods are gone then what are people channeling when they recite miracles to the gods?) is because it’s actually reused content and ideas from Demon’s Souls, where things mostly all made sense. In this case though, it was probably because they came up with the general idea of “burnt knights” early in development and just threw together an explanation near the end. FromSoft tends to come up with ideas first, rationalizations later. If specifics aren’t clear, it’s not always because of storytelling. Sometimes it’s just because they didn’t give a shit and just threw it in there.