The SI joint is the joint between your sacrum and your ilium, parts of your pelvis. It's there to allow a little motion, (only about 12 deg each way at each joint if they are healthy), so that torsional forces during leg movements can be dissipated, especially when walking or running. Without them in combination with the pubic symphasis, our pelvis would be one solid bone constantly under torsional stress and getting microfractures. Not to mention the important role of the SI joints in childbirth.

Sometimes this joint can become dysfunctional by moving too much or too little. This can lead to all kinds of compensation during movement and will result in pain locally and/or elsewhere... knee included. So yes, if your PT hasn't looked at your low back-pelvis-hip mechanics. It's worth having them check it out. A messed up SI often goes right along with the "dumb butt" syndrome Knott mentioned earlier.