pain behind the knee

I had pain behind the knee but mine was caused by a leg length decrepency.  I found out it was two things causing it, my seat being too high on my bike and also over striding when running.  It was only on the left leg which I found out was shorter by a couple of cm.   For the bike, I learned I had to lower the seat to help not overextend the left leg.  For running, I had to not over extend my stride and keep it smaller. 

My pain was towards to upper behind the knee, closer to the hamstring, but I think it was a tendon or something.  It was not a muscle I don't think. 

How I figured it out was, if you put your bf on any bike, put the seat at a height he can reach where his heels are flush on the pedal at the lowest bottom position (6 oclock).  Then raise the seat ever so slightly, have him get on again.  Keep doing it.  At some point, if one leg is longer/shorter, one heel will touch the pedal at the 6 oclock position, and other will be slightly off the pedal when you rotate it to check that 6 oclock position.