Settling occurs when the paint pigment falls to the bottom of the bottle. All paints tend to settle when they haven't been used for a while. Modeling paints are notorious for settling while you use them the end result being that the color you finish painting with is not exactly the same as the color you started with.
Use the following trick to maintain a consistent color while painting.
The paint on the lid is sufficent to paint with but there isn't enough there for the paint pigment to settle out since a dab of the brush will always go to the bottom of the lid.