If this is a new area you'll have to check the layer display settings in MapSet to include it. To do so, in MapSet, add the layer to your map. Then, click Options > Layer Display Settings.
In the Layer Display Settings Window, click the Polygon tab, then click the Select button under Color Classify.
You can verify the colors here. I usually click Apply Random Colors.
If that doesn't work, you might have to call Central Square support. MapSet is so awful I usually have to anyway.