I had a somewhat similar problem a long time ago. One winter I was playing basketball and smacked my knee into another player's knee - was a little sore but didn't think much of it. That spring, on my first ride, my knee starting having a sharp, piercing pain behind the kneecap after about 2 miles of easy spinning. Gave the knee a rest, tried again with the same results. Only bicycling caused the pain, I figured it must be related to the frequency of motion. Every spring I tried to get back on the bike, but had the same outcome. 8 years after the first occurrence I finally started being able to ride, not totally without pain at first, but 3 more years later I was fine. I didn't have the knee checked because it only happened while cycling, and didn't feel that it was important enough to go through any procedure to get it fixed, if it could even be repaired. Someone in the physical therapy field did suggest that perhaps the knee collision altered the kneecap "track" and caused inflammation until it worked itself out. Not sure about that, but the fact that the knee healed itself after a while tells me it wasn't a major structural issue. Like the OP, I had no changes in the bike that would point to fit issues. In fact, I was riding the bike for at least 5 years with absolutely no knee problems, and when the knee started feeling better, I had not changed anything