I used to play a lot of squash and enjoyed running until my knees said "no more".I think it is the combination of old sporting injuries, I did play a lot of football and and squash up until 10 years ago. twisted knees and dislocated patella, rhs, 4 times. still, as I said, I doesn't impact on the cycling, yet.
I now take daily cod liver oil tablets. Some people say they are rubbish but I have not had knee problems for years. Of course, I dont run or play squash now so that will help.
Hope it gets better but at least, as you say, you can cycle.