Do you keep your back straight up and down throughout the movement? I just started doing these (set at a point I'd estimate to be about two inches below parallel) and I'm finding I have to be stricter with my form than I do with regular squats. That's fine - improving my form is the whole point of doing them. I've just always wondered how much of a forward lean (if any) is permissible with these. These issues seem to resolve themselves when I do regular squats - everything just sort of lines up on its own. I do find that that mythical "just below parallel" mark is always, always lower than I thought.
