If you are certain that this clicking occurs only in later tracks, then it is due to the burning process. As you move outward from the center of the disc (the direction of data read/writes) it becomes harder to track the disc as the disc wobbles a bit more and the data is read/written more quickly.
Try burning a disc with the burn speed turned down. In general, don't pick the very highest rated burn speed for your CD player. Burning at a lower speed yields a higher quality burn. Different CD players exhibit varying sensitivity to this behavior so for maximum compatibility, use a lower burn speed.
Also make sure that the CDs you are burning support whatever burn speed you are using.