Are your heels elevated when you do this? I've found that, for now, I MUST elevate my heels to do a proper deep squat of any kind. They don't have to be elevated much - a fraction of an inch will do - but they must be elevated.
My trainer has given me a corrective where I reach down and grab my toes, then I go in as deep a squat as possible. Then, still holding onto my toes, I very slowly raise up until my legs are straight - I count to five while raising my rear end. Then, not letting go of my toes, I do it again, 10 times total. This has/is really helping my flexibility and the depth of my squats. For whatever reason this is proving more helpful to me than simply holding a deep squat - that I do that as well.