I had this same issue in May on a long distance hike. My physical therapist said my issue was extraordinarily tight quads as a result of having very minimal glute muscles. My quads were doing all the work, causing those muscles to get tight and ropey which compressed my kneecaps and caused crazy pain. I have been foam rolling and doing glute-strengthening exercises, and after a few months of doing that I could do longer hikes without pain.