I have the same issue cheesecake, I'm using Stock Size RSS and anything I create with KK ends up partially or completely buried. Oddly enough, opening KK and clicking on an instance snaps it back to where it should be. I assume this has something to do with the scaling but I'm not sure how to help resolve it?
edit: may also have to do with the loading order of mods (i.e. KK gets loaded in before the terrain adjustments are made?) I'm not sure here, just guessing in the blind?