I'm still a super-rookie too, so take this for what it's worth, but how is your calf flexibility?
The way I'm picturing what you're talking about, it sounds like when you do free-standing squats you're leaning really far forward to compensate for the fact that your knees aren't coming far forward enough. With your knees staying back and your shins staying relatively verticle, your hips would stay farther back than you want for an olympic squat. Keeping your back upright might then cause your balance to be way too far backward, unless you could lean on something. The shear angle of your torso when you compensate and the position of your knees would however get in the way of you getting deeper into the squat.
Does this sound familiar, or am I way off base?