scheduled operators have two sets of codes and charters who do not operate scheduled services just one.
All airlines have a 2 letter identifier set by IATA and a 3 letter identifier set by ICAO.
E.g. Britannia and My Travel are both charter airlines. Britannia's codes are BY/BAL. They use their 2 letter code for their flight No's where as My Travel use VZ/MYT and they use their 3 letter code for their flight No's. So the theory on charter/scheduled using 2 and 3 letter codes is thrown away on that one as the airline can choose which identifier they want to use.