The only time I've had knee problems is when I rode 100 miles in two days on the Blue Ridge Parkway. I was so worried about all the climbing that I kept my gearing in the granny gears. The second day was the worst. My riding partner suggested that I push slightly harder gears (not mash, just not spin with abandon) and that really helped. It seems counter productive to push harder gears to keep knees from hurting, but it worked for me. Were you spinning with abandon on your long ride?