When the game initially loads, the mod creates new textures for each block. This processing may occur earlier than when all of the vanilla textures have been processed by the ResourceManager.

I for the life of me can't figure out what causes this to happen. It seems to be completely random. You could launch the mod 3 times in a row with no issues, but the 4th time will bug the textures.

The bug was in TextureAtlasMixin.java. The textures haven't been mixed yet, but it only needs the size of the texture (Same as underlying texture).