I've noticed this issue since before the biomes update. if I decide to do some ground leveling in my area, i would sometimes use the pickaxe to quickly take out chunks of the ground to the approximate level I want and then use the rake to level it. One issue, however, is I expose stone or other material unde the dirt layer so when using the rake, only the dirt area levels but other materials lower than the dirt turns into a hole. I've tried filling the hole with dirt and re-raking but it partially works and I usually get another hole. I think the issue is that some of the underlying material under the dirt is still exposed and the rake is only modifying dirt, not any other texture.
My work around was to switch to creative mode and paint the terrain with the dirt texture so no more of the underlying texture is exposed to the surface. I can then rake just fine afterwards (or use the smooth tool in creative mode since its much faster). This issue is much worse in the savanah biome where there's dry dirt underneath the normal dirt. In a grassfield or forest, i usually had not much issue covering stone with dirt and raking. Its become more of an issue with the new biomes and additional subsurface textures. I'd like to be able to fix the terrain to my liking without having to resort to creative mode.
