Without taking a look at the configs related to that I cant say much.
But it seems like you have some issues with the Biome Sizes.
Biome Groups, Biomes, and IsleBiomes need to be drawn in the right order. (BiomeSize)
You need to picture yourself in which order it needs to be drawn, and set the sizes accordingly. Lowest size first, Largest size last.
IIRC, the order is:
BiomeGroups, Biomes, IsleBiomes, BorderBiomes, for each size.