I think Gregorus is referring to the smaller, darker lakes in the middle of the map. They appear to be very pixellated or maybe had a layer of noise added to them.
But overall this is coming along nicely.
Ah! Right, now I understand. Yeah, they've come out rather odd, even though they've had exactly the same treatment as the rest of the map. It's probably something to do with the initial stage of creating the landmasses. I hope I can do something to them by fidgeting with the layers I've already got - I rather like the way this one's heading and don't really want start over now (I will if I have to though).