Guessing you painted multiple textures in one area, you can only have a maximum of 6 in one cell, click on the ground where it's black then press the i key to check.
Where textures are concerned, each cell is split into 4 quads and you can only have a maximum of 6 textures in each quad. Theoritically, you could have a maximum of 24 textures in each cell, but due to overlaping textures, I'd say that probably the most you'd get is around 18 textures per cell.
To rectify, press
i when the landscape window window is open. This will give you a new window with the layout of the 4 quads and the textures in each. The best way to fix is to right click the texture with the lowest percentage and replace it with one of the other textures that appear in the quad.