First, if the weightlifting shoes are making things worse, STOP WEARING THEM!
If chucks aren't letting your knees get beat up as badly, then wear them.
Secondly, this could be anything really. Sticking point wise concentric only squats off the safety pins from your sticking point will help. Valgus wise it could be anything: often times people with good mobility are either a) compensating elsewhere and thus disguising a mobility OR stability deficit at a vulnerable joint or b) not creating enough stability in the first place.
Could be your program, since we don't know what exercises, sets/reps/weekly layout look like, could be lack of strength in posterior chain with overcompensation, could be tightness somewhere (especially quads, TFL, IT band), could be a technical problem that is pitching you forward onto your knees, could be a ton of things. If your hamstrings are in fact weak, then you need to really get them up to par ASAP. Especially as you are experiencing problems at the knee joint, this might be a good time to switch emphasis and work on a KNOWN weakness that will also most likely help stabilize your knee joint and the tensions from the quadriceps. You may end up surprised at how much it helps.
You'll likely also be surprised at how much glute strength and releasing the hip flexors help as well. Regardless, get away from the pain for a bit and focus on known weak points. Worst case is they help you once you get the problem at your knees figured out...which is to say, working the weaknesses will help regardless either immediately OR down the line.