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If it doesn't hurt when you do body weight squats with zero weight, then you can make it not hurt when you do heavier weights. The trick is to start with body weight squats, or an empty bar, and build slowly. At every step, keeping proper form. Adding only 5 lbs each workout. So many people make the exact claim you're making, without actually going through the painstaking process of starting from no weight on the bar…
I can do body squats fine (lots of popping, though). I've worked up in weight (though not quite from empty). One week I'll be able to do semi-heavy squats (not even my bodyweight) with no problems and then the next two weeks I can't even add much more than the bar before the knife-in-the-knee. Both knees have the issue, and not simultaneously. The physical therapist says I'm a bit pronated, so I try to account for th…
If you can find an FMS certified strength trainer, there's a good chance they could help diagnose your situation. http://www.functionalmovement.com