Can't help you diagnose, but I have recently been in to see a PT re: knee issues.  I had pain under & below the knee cap - and pain when running up or down hill (or walking up stairs).  Diagnosed by PT as patella tracking issue.  He gave me a set of basic knee strengthening exercises.  He also was able to pinpoint the muscles that were weaker and causing the kneecap to not track right, so the excercises focused on those. 

To continue running while strengthening, he showed me how to tape my knee - taping the kneecap in a position where it will track right. It took a while to get the hang of it and get it in the right position. To test whether I taped it right, I step up on a step and if it doesn't hurt any more, it is right. It was miraculous the first time he did it - I stepped up without the tape and it hurt. Then he taped it and I stepped up with the tape and it didn't hurt. Amazing.

So that's my story - I would recommend finding a good PT to get it formally diagnosed and treated right.  Too much to lose with knee pain.