Patella Tracking/Runner’s Knee

Hello, I have a slight case or runner’s knee, which seems to be on the mend.
My patella, however, seems to go off track near the end of a long run.
I am dilligent in working my legs, and have very strong vmos. Nearing the end of a 1/2 ironman I did, the patella seemed to be clicking on the inside of my leg.
There was no pain accompanying this. Could my patella be hitting bone, with no pain?
I’d guess this is due to muscle imbalance, but which exercises would cause the patella to pull to the outside/inside?
I went to a sports doc, and he said not to worry–as there is no pain.
I just got back from a 12 mile run, and near the end the click was there, less than before(due to the fact that I’ve been resting), but still there. Am I destined to live with this, or is it a condition that will get better with rest?
I run in motion control shoes, and tend to overpronate a bit.
I’m 29, and weigh 175.
I have completed 7 marathons(and don’t want to stop now), with no trouble at all.
I begun doing triathlons this year, and am wondering if all the added biking/swimming has led to the muscle imbalance. Any help would be greatly appreciated.Thanks,Chuck