Cruciates don't affect the kneecaps, they make sure the tibia and femur are attached properly.
There's a layer of cartilage on the back of the kneecap that allows it to slide smoothly as you bend the knee. If you have any restriction on how you knee moves, or an imbalance in how your quads operate on the kneecap, you can end up with it not tracking quite right. If that happens, you can put too much pressure on this structure and it can hurt. I am susceptible to tracking problems - I find that if I put my legwarmers on a bit wonky, or if they are mega tight, then I get knee pain.