This can be an annoying problem. Fortunately, you are making your own tileset, not using someone else's, so you have the ability to fix it! Place this tile into your tileset:

Now, set layer 8 (or 7, or whatever you're using) to "Tile Height" and use that tile as the bottom of the layer. You will probably need to edit the diagonal line part to tile properly with the rest, but that shouldn't be too hard.