Actually, they did not change. At the beginning, Spanair was a charter only company. They had the indicative SP (IATA) and SPP (ICAO). When they started to operate scheduled flights (first only air shuttle MAD-BCN and BCN-MAD), now many destinations even to/from Europe and North and Sotuh America (mostly Brazil), they started to use a new code for distinguishing theese flights from the charter ones: JK (IATA) and JKK (ICAO).
Actually, they still use both signs.
For those who like to listen to ATC, even the callsign is different: Spanair for scheduled flights and Sunwind for charter ones.