As you know from time to time I go on a long hike through some mountains that last days.
On my first such trip I had no problems, but on the second I eventually started feeling a pain in my left knee. I attributed it to the long hike and me basically overusing that part of my body. On my last trip I really injured my left ankle - it put me out of commission for about a year and a half. There was no "Ow, I twisted my ankle" moment or anything, it just started hurting one day on the trail, and hurt more and more on my trip. I aggrevated my injury one morning at a hostel too by stumbling out of the bathroom in the dark and forgetting that there was a 15cm drop in the elevation.
Anyway, I finally went to see someone about it after I returned from that last trip, because the pain was quite bad. The experts concluded that I "walk wrong" - the shape of my knees, feet, and the rest of my frame was off... because I have flat feet. This, according to them, affects the way not only the way the bones and muscles in my feet are angled, but also the way parts of my knees are angled, spine, and so on. This is usually not a problem, but basically certain body parts get an undue amount of pressure, because they're angled wrong, and the parts around them are angled wrong as well. So basically if I'm on a demanding 5 day long hike, eventually certain parts just can't handle it anymore, and apparently that's what happened on my last trip - a tendon just couldn't handle the repeated pressure and gave out, and then I couldn't play soccer for a year and a half. And apparently that's also what lead to my problems with my left knee on that other trip. This whole "you walk wrong because your feet are flat" thing messes up my whole body is angled in some places - it affects a lot more than just my feets. And usually I don't put any repeated pressure on these body parts, so I haven't noticed any real problems until I started to.
So basically now I wear orthodics in my shoes - this is supposed to angle everything just right and prevent those undue stresses to parts of my body. So maybe you should get your feet checked out and see if you could benefit from orthodics, because.. well, it's the reason I don't jog (reason #2, I'm lazy). My knees aren't perfect due to the wear over the years, so I just don't want to aggrevate them any more. No idea if your feet are flat at all, but if they are even a bit, orthodics would probably be a wise investment, especially if your health insurance will cover them.