Ok, I was re-reading Rip's book, and it talks about an uneven bar placement. I don't know if I had an uneven bar placement, but the bar I was using was starting to fall apart, and the shoulder thing that keeps the weights from sliding in was broke and while doing my sets it would pop off and let the weights slide in a inch or two. The uneven weight distrubution from this would be similar to an uneven bar placement.
If this caused my knee injury, which still hurts anytime I approach parallel, what sort of injury do I have? How should I treat it?