Do your hip flexors hurt?
I had some kneecap pain when I lost my lumbar curve, my weight shifted to the ball of my feet, and my torso shifted forwards in order to get proper depth.
Getting depth (in a relaxed squat) is one thing...
(Proper mobility for that took me months)
Maintaining tension in your muscles so you retain your lumbar curve and get a full stretch of your hip flexors is another thing...
(I'm still working on it)
There is a fairly recent T nation article by Ripptoe on maintaining lumbar curve. Maybe check about that? That you know how it feels to hold that lumbar arch tightly. A lot of people think they are maintaining their lumbar curve - but they aren't (because the hip flexors are too tight).
For quite a while I thought the problem was that my hip flexors needed to be stretched (lunge stretch, quad stretch etc). That only pissed it off and it got inflamed (burning type of pain).
What helped me the most was front loaded plate squats / goblet squats. Basically hold a plate or dumbell out in front of you (enough weight to help balance you) then try setting your lumbar arch as tight as you can and slowly pulling yourself down with your hip flexors (if that makes sense). You should be able to feel it when you hit your bottom position for now - and gentle bouncing should help push it lower. Gradually. Over time.
Hope this helps.