If the "inner" knee pain you're feeling is medial and lower than your kneecap, the pain your feeling is most likely from the Pes anserinus or in other words the attachment of the Sartorius, Gracilis and Semitendinosus aka Hamstrings. I have had pain in this location after riding a road bike instead of my usual tri bike. I could totally feel the difference in hamstring recruitment and this left me sore. Hope this helps.