What you're seeing is about as good as FT can do for level terrain areas. FT uses a resolution-independent fractal function combined with fixed-resolution editing channels. The final altitude is calculated approximately as

altitude = (fractalfunction + prescale) * roughness + offset

The fractal function wiggles at a much higher frequency than the editing data. When you try to do things such as filling basins or setting altitudes, the system computes the altitude value as above for each editing location and then adjusts the offset value by the amount needed to make the final altitude output equal to the specified value from the fill operation.

The lack of smoothness stems from the fact that the fractal function is still wiggling around between the editing points. So even though the editing points will be at the specified value, the places in between the editing points will still be trying to do what it originally did, resulting in the bumps.

It is possible to force FT to eliminate the fractal function by evaluating the altitude once, setting that altitude into the offset channel, and setting the roughness to zero. This operation is performed via the Tools>>Actions>>Burn In To Surface. However, your surface will then be fixed in resolution whatever your specified editing resolution is. You can do fills, basin fills, and other operations just as with Wilbur and without trying to fight the fractal function contribution.