These look pretty good to me. I don't see any obvious cause of trouble to the knees, but you said this stance and depth is a little different than you had been doing, so it could be that you've fixed the cause of the issue. Your stance looks right and your depth looks ideal (to my eyes) for low bar squat. You do a great job of keeping the knees out... possibly even too good of a job? They are pretty far out and you have them there throughout the reps, at least on the view from the front... most people have the opposite problem, so I hesitate to steer you back the other way, but just make sure your knees track your toes and you're not tracking way outside or at a different angle than your feet. I would recommend lifting shoes for this particular type of squat but you seem to be OK without them (you'll do better knee-wise and strength-wise if you wear lifting shoes, IMO).
Two other things that caught my eye, not likely related to your knees but other opportunities for improvement: 1) Get under the bar to rack and unrack. It's out in front of you currently, so you have to lever it out with your back. Get wedged under it and squat under it, stand up, then step back with a minimum of foot movement. This all gets more important as it gets heavier. 2) Use your breath more to stabilize your spine. There are times you look a little wobbly between reps, and you could take a bigger breath and get tighter for each rep. I see you brace the torso muscles, but put more focus on the breath and diaphragm to make your torso tight and strong along with the abs and back muscles.
Two other things that caught my eye, not likely related to your knees but other opportunities for improvement: 1) Get under the bar to rack and unrack. It's out in front of you currently, so you have to lever it out with your back. Get wedged under it and squat under it, stand up, then step back with a minimum of foot movement. This all gets more important as it gets heavier. 2) Use your breath more to stabilize your spine. There are times you look a little wobbly between reps, and you could take a bigger breath and get tighter for each rep. I see you brace the torso muscles, but put more focus on the breath and diaphragm to make your torso tight and strong along with the abs and back muscles.