Originally Posted by Tamara Cohen
Cue yourself to keep your chest tall and drive out of the hole with your elbows. This will help keep the bar over the middle of your foot.
I think Tamara hit the nail on the head here. I think it's hard to say that you have a muscle imbalance when you really need to keep your chest up. Think of the body as an entire unit: if you have slack in your chest/upper back and you sink in the hole at the bottom of the squat, other parts start moving incorrectly (i.e knees come in, ankle rolls slightly off the floor, elbows come forward knocking you off balance). When you do keep your chest up, you might find that you can't squat as deep and then it would be prudent to look at the lower half of the body.
Check out the Catalyst athletic warm up and mobilitywod.com and keep trying to get better ankle and hip mobility but I think you should really work on t-spine mobility drills and the tricep smash to get your elbows up better and have a better front rack.