How do you know that your legs are different lengths?
Has this been confirmed by a doctor? What is the cause?
You may need to see a chrio for a hip adjustment.
Are you addressing your hip flexors and hamstrings?
These restricting contribute to squatting to one side.
Your body makes adjustments to complete the movement.

Addressing the tight hip flexors and hamstrings will help the issue.
It may not completely solve the problem, but you need to start working on it.
If you are working on things and not seeing improvements you need to re asses the situation.
Pro Episode # 21 – Pro-User Request Friday: Not Seeing The Change? You Need a Systems Approach.