Apologies for resurrecting an older thread but I'd just like to know how or if you managed to resolve this problem since I'm having the EXACT same issues you describe in your first post.
My pain only occurs when walking for longer than about 5 minutes, but other than that, there is absolutely no pain or problem with it. I can perform bodyweight squats, walk up or down stairs, there's no pain at all when I prod or poke the knee, in fact I can be as rough with it as I like without feeling even the slightest twinge of pain! But should I walk on it for 5 minutes or so then I'll begin to feel something then if I continue walking for about 10 to 15 minutes I'll basically end up limping in - if not agony then reasonably - severe pain.
From my utterly amateur, internet based self diagnosis it looks to me like some kind of low grade medial ligament tear, but I'd love to hear some follow up info from someone who has already experienced this issue!