Just some ideas.
I know that hiking for me, especially with a pack is the absolute worst thing for my knees now. After our last backpack trip, I was in pain for almost a month afterwards. This is what prompted me to go see a sports podiatrist.... a gait specialist. He gave me an athletic shoe prescription, and the IT band stretching program.
Not that you need an orthotic, but... the type of shoe you are wearing, and how it controls rotation, supination, pronation and all that stuff can make a huge difference on how your knees track over your feet while moving around.
Just a thought...
Irulan
2015 Liv Intrigue 2
Pro Mongoose Titanium Singlespeed
2012 Trek Madone 4.6 Compact SRAM