Looking a little closer at the rivers, and I see you have a common issue there too - you have rivers flowing into lakes, with out outflow. FT runs a river until it hits water. I have found a quick workaround is to lower your water level to -1000, run the rivers, and then restore the water level to 0. If your rivers and water are the same color, the rivers will be invisible as they go across the lake's location. It is hardly topographically accurate, but making accurate rivers is a major undertaking even for advanced users.