The Ready State Virtual Mobility Coach is like having a virtual Kelly Starrett in your pocket.
I have a similar problem; although for me it seems to be that my hips are crooked, especially at the bottom of the squat (low bar back squat). I can squat down nearly straight, but as I start to ascend, I seem to shift over to the right slightly. The heavier the squat the worse it gets. Previously my left knee would cave in as well. I did a massive reset (taking 75 punds off the bar) and built back up, which fixed the knee but that slight shift at the bottom still keeps happening. Have you seen this before? What is the issue?