The drier you skim the darker the skimmate will be, sock or no socks. The chunks you're seeing is where the dry skimmate is clumping together to form a film. When that film gets thick enough it falls down into the cup. When things are normal you generally want to skim drier. Since you're seeing that nice dark brown, almost black, skimmate, I'd say you have it tuned just right and it's running great.I'm surprised at how disgusting my skimmer cup is (almost black) considering I'm swapping out the filter floss every few days that is a deep brown with lots of little chunks in it.
I think the combo is one major factor in my nitrates being 0.25ppm, but as @anit77 says, mine is certainly a new tank. I plan on throwing socks of carbon in the cups from time to time, but I'm not sure if I'll ever remove the floss completely considering how much my kids love to feed the tank.