I look in the editor, and the colors for various texture masks isn't the same as what gets saved out. For example my sand layer in one instance is blue, and in a small basin where water is. I look at the PNG saved out and it is red. It looks like the red and blue channels are not swapped correctly.
Anyway I have a tool that combines alpha maps into a single texture atlas so I am currently swapping it in there, so this isn't a huge priority, but may be work looking at. This occurs in 2.4b Rev. 2.