1) Even though you tested the cable by using your MP3 player, I suggest you check it for shorts while bending or moving the cable around, especially at the point where the molding meets the connector.
2) Without knowing much about your speakers, check to see if the crackle or problem sound is only coming from a single driver. So listen to each speaker at the driver points (tweeter, midrange, woofer). If the crackling is coming from ALL drivers, then you have some sort of input problem. If the crackle comes from a single driver...well, there you have the problem.
Hope this helps.