Could this pain be a lack of running?

cmac

I trained all during last winter (Nov - Mar 17) for HM with no issues. I ran 2 HMs mid and end of Mar and was in great form with no niggles. Two weeks later I developed knee pain on the outside of my right knee. It was very localised and sent shooting pains up my leg into my glutes. After a mile I couldn't run and barely walk.

Was treated by physio for tight IT band, rested for about 12 weeks, took up swimming and did regular hip strengthening exercises.

Started back running and now I get very odd and inconsistent on/off pains around both knees (while running or sitting). Sometimes the left sometimes the right and can be interior/ exterior or below the knee cap. I am back running about 6 weeks and even ran a 10 mile race last week. I'm continuing to stretch and given that the original pain is not the issue could I assume these are pains from my legs retraining since the lay off and strengthening works?