Ok I see now what is the probelm, if you take a look in output/flatten_terrain.pgm all the areas marked there become 1 foot elevation.
See:
https://www.hitechcreations.com/wiki/index.php/Terrain_Generation_From_Geographical_Data#Handling_Water_BodiesI explain why, the AH water bodies model is defined by terrain elevation, anything above 0 is ground, below is water. So basically it means that every water body MUST be placed at sea level, i.e. altitude = 0. If course it is not the case for real terrains. So makeahmap performs recalculation of altitudes that preserve as much of terrain "texture" as possible but it means that if there area near a river that is actually lower than the level of the river it will be pushed below 0 and thus flatten to be a ground.
Unfortunately I don't have a solution for this unless you remove your water bodies.
There are two parameter to control this
1. water_alt_limit that would remove water above certain altitude rather than bringing it to 0 altitude and thus do less deformations to the terrain - try values like 500 to 2000 and check outputs to see flatten terrain/map to see water bodies vs flat terrain.
2. You can also keep only largest rivers by setting river_level to lower value 2 or 1 (default is 3). It prevents lots of flatten areas but you loose some smaller rivers.
So play with these parameters and check output/flatten_terrain.pgm and output/water_bodies.pgm to see the effect, take a look on clipboard map too see how it looks like
And you right - no need to adjust the water to land slope/range - it is a different thing.
Regards,
Artik