How did you transfer the beer to the fermentors? Which was first and which was second? Did you chill and settle in the kettle first?
I don't have any data about yeast impacting color, but it seems unlikely to have any significant impact. I'd be much more inclined to look at things that would impact wort composition. Wort tends to stratify pretty quickly, so with any settling period I would imagine you could see darker (and likely higher gravity) wort settling to the bottom. As you mentioned, trub in suspension could also have an impact, but that should settle out.