Sounds like IT band problem with knees. Overuse of the knee in the incorrect position. I would raise the seat higher. If you are going to ride long distances I would raise the seat all the way up until you are not comfortable and then lower it a little so hips would stop rocking. I just went for a 138 mile very hilly ride and my knees started bothering me(IT band) at mile 80-90. I though my seat was high enough, bit it was not, I had to raise it a little and knee pain went away for the rest of the ride.