First order of business is to be sure you do not still have an ongoing injury to the knee. A visit to your doctor or orthopedist should fix that. If it's not your knee, then it could be any combination of any number of things. Seat height, seat forward adjustment, crank arm length, shoes, pedals, wedges needed on your shoes, etc. See? could be anything. You need a really good fit. Not just driving up to a lbs and asking for the owner to take 15 minutes and fit you, but you need a really good fit. There are two or three that are very, very good. Retul fit and BG fit are two I recommend. If you're riding one bike and it doesn't hurt, but your road bike does, then it's the way the bike is set up. Cycling should cause suffering, not this type of pain.