SGB palettes aren't recognized by the CGB, which instead only has a hardcoded set of 12 to apply on regular GameBoy games. Backwards-compatible CGB games used another incompatible format. Some games (Pokémon Yellow) contained both.
If you want you can see all the gory details in The Game Boy Programming Manual (huge PDF):
http://chrisantonellis.com/files/gameboy/gb-programming-manu...