I'm not sure if it means anything but here's my experience.
I weigh 155 and I started squatting at about 165. When I first started my knees did the same thing, they would get a lot of pressure or discomfort or something in them, and I would have to pop them, I couldn't even sit for very long without wanting to stand up or something. (sound familiar?)
Anyway, I started looking into it, and a Physical therapist said that this is probably nothing to be too concerned about. The knee joints have to work a bit during squats, more than they are used to at first.
The biggest thing for me was that my hips were not flexible enough. It was a flexibility strain to stand in the squat position for very long with no weights, so my knees were having to compensate. I started stretching my hips after every workout and that a big difference.
Some other workouts I did (they all helped) were: Goblet squats, leg press, sprints, high box squats, and leg curls. I have, however, kept good 'ol back squats as my primary workout.
I now squat 245(still not to impressive), but My knee discomfort is completely gone, my knees have stopped popping, and even better, my toes have straightened out when I walk (I used to be the extreme opposite of pigeon toed). I looked like a ballerina with my toes pointing straight out.
I think, if you are squatting with right form (knees over toes, shins 90 degrees to floor, straight back, etc.), you are just waking up the joints and the stabilizing muscles around the knees. It was weird at first for me too, but having worked past it, my legs feel much stronger and more stable. Not to mention my squats are starting to go up a lot faster.