Sounds like you might be running into a problem with map rotation. I started out by using my black/white map to help shape the terrain (wanted the walks to be flat, ground to be lumpy). That worked fine. Then I used the same image to drive the distribution of 2 materials. The distribution didn't match up until I rotated the driving map 180 degrees. When I added my map driven ecosystems, again I had to rotate the distribution map.