I had tendon problems last year went to pt for 3 months. I still have knee problems. Could the problem never have left me?

Strengthen your quad. What stabilizes the knee especially if you run, are your quadriceps. Strengthening your thigh muscles with weights will stabilize your knee cap and you may have significant less knee issues. Doing pt for 3 months is great, but you need maintenance with regular muscle strengthening exercises. Hope this helps! Also look up patellar femoral syndrome.