Is transparency enabled?
Also, SAI does not do a proper grayscaled image. I would suggest you go into GIMP, create a new file the same size as your height map and then copy and paste into it. That way, it is grayscaled for sure. Just because you used blacks, greys, and whites, doesn't mean it is grayscale. The file itself needs to be grayscale. Most likely, from the info you have provided, that is your primary issue.
As for the program, I do not know of any sorts that would offer a simple way. Since FeralHeart runs on a rather old engine, I wouldn't imagine there is anything that works. On second thought, maybe you could sketch up a concept for you to follow. That is what I do, I draw a bird's-eye view of the map, work in certain special details, and make many notes of where to put things exactly. (: