While designing a terrain I had to face this issue. Loading the alpha map(materials) as it is to the height map was caused to an issue. After the alpha map was loaded to the height map, I was able to figure out that there was a miss match on those two. Latter on I did a trial and error testing on these two maps and figure out that the alpha map must be vertically flipped before loading to the height map which is demonstrating on following figures.
http://i.imgur.com/uk1Pu.jpg
when loading in the alpha using the Asset Manager map you will want to set the TextureKey to flip the Y value.