By default, mod biomes are assigned a colour that is equal to their biome ID, but these are not added to the internal mapping. As a result, if left unchanged from the default colour, they're not recognized, and will fall back to the undefined biome. If I change the colour to something different from the ID, it works correctly.

Does this sound right? Maybe this line should simply be the following?

if (this.useCustomColorMappings == true)