The most likely thing that will cause Fill Basins to flatten your map is that the map is roughly in the shape of a bowl and Wilbur is filling the bowl. If you're not careful, it's possible to get the outermost ring of pixels higher than the rest of the landscape. Then Wilbur will see the whole map as a basin.

As far as the parameter for fill basins, it has two main ranges: less than 0 (Wilbur will calculate a value for you that is greater than zero based on surface dimensions and the desire to avoid perfectly flat fills on the basins) and greater than or equal to 0, where the parameter will determine the slope in the filled areas (0 is completely flat).