I never have knee pain when road riding (I ride anywhere from 15-20 hours a week). I've been doing a lot of mtb riding this week (3 hours racing on Sunday, 2 hour very technical ride on Wednesday, and a 1.5 hour not-too-technical ride yesterday). I've noticed just a bit of knee pain lately and it has nothing to do with strength or flexibility or bike fit. It has to do with how we use our joints (hips & knees) when we mtn bike. For more technical riding, we put a lot of stress on our joints as we steer the bike around switchbacks and on climbs & descents. The sport is much more demanding on our joints than road riding where you track in a straight plane.