Could be lots of things, do suggest another fit adjustment now that you have ridden a while and see symptoms of the fit. Generally tops of knees means you are under-extending - I had the same problem, the tops of my knees were hurting walking up the stairs after rides (esp after a winter of indoor riding where you cann't move around much) and I raised the seat a couple of millimeters and it helped considerably.
Just one idea though, you should see about another adjustment, it's common to do once you've ridden and your body adjusts. This is barring other factors but just conditioning shouldn't cause that kind of pain provided you did not have really bad knees to begin with.




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