The old adage is "Pain in front of knee, raise saddle. Pain in back of knee, lower saddle." So the problem could have started because your saddle has been too low all along. Makes sense when one realizes that the greater the knee bend, the greater the down force on the kneecap. Thus spinning on the climbs or climbing standing are also good for the knees. One can also reduce force on the kneecap by smooth pedaling rather than hammering the downstroke.