I've never seen that behavior before. Judging from the black spot disease in the first image, this data came from Fractal Terrains Pro via an MDR file, correct?

In Wilbur, if you do Window>Histogram, what does the system show for the low and high values?

My guess is that the black spots represent infinities, which will completely eat your surface from a fill-basins perspective, I think. If your version of FT doesn't have the Tools>>Actions>>Normalize Data feature, try pestering ProFantasy tech support for version that does, then use that tool. I will try to remember to add a similar tool to Wilbur, but I don't know when I'll have time to get around to it.