Cant really see exactly what you are doing, we need a video shot from the side. One thing i can see is you are doing your box squats incorrectly. You need to sit back on the box and pause, relax your hips, and explode off the box. You are just squatting down to it and touching it with your ass. The whole point of box squats is to build power in the hips to get out of the hole. Take another video of you squatting from a side view so I can really break down your squat.
if yuo read the description on my YT video, it says I was just using the box so that I knew when I was at parallel. I realised after that I was about 1 inch above parallel or less. These weren't box squats.
Ill get a some better vids on monday though.