Make the focus on your glutes. Next time you squat, put the camera in front for a few sets and see if your knees tick in at the bottom. I think that's what's happening. It's like Sean said a few posts ago, stay TIGHT in the hole. You did a great job of pushing your head back out of the hole, but I think your ass is taking a nap right at the very bottom.
EDIT: Speaking of taking a nap in the bottom! Add in some pause squats again. Like, in your first couple warmup sets, put a band around your knees and hit some pausers. Then as assistance or on upper body days, hit some slightly heavier pauses. If your knees want to cave, hit 'em with the band again.