I mess with the population settings more than just about any other part of Terragen 2. I have only seen this occur if the program is calculating something else, like a heightfield. The only thing which may cause this other than that is if a calculate terrain or calculate normal is linked to the populations blend shader someway.
You may also want to be sure that a blend by shader input is getting only color information if you are using functions in some way. I crashed the program the other day messing around by not making sure this is right. (Actually, I crash the program quite often while trying to use functions. I don't understand them enough, but I am learning what not to do.)