My problem was knees to far BACKWARDS.
Knees were drifting forwards at the bottom. I read in a few places that this could be fixed by setting knees forward into final position during the beginning of the squat.
This confused me somewhat and I was doing the weird two-part squat for a few sessions.
But now I think I have fixed it by using a wider stance, knees pushed out A LOT during the beginning of the squat.
My squat looks a lot smoother now with descent and ascent both at the same speed even though I am now pushing maximal weight.