While I can't know for sure, weakness in my glutes (especially med) were causing unnecessary & unnatural load going through the knee during the gait. While this wasn't a major imbalance, it added up over time due to my high mileage each week. Once I became more disciplined with glute-specific work and more hip stability, I was able to improve my running economy just enough to put less stress on the knees and alleviate the pain.

Hope this helps.