Hi mate,
i'd go and get it checked, the action of cycling is actually slightly unnatural for yours knees as a lot of peoples knees point out slightly. I had lots of problems and went to a shop where they sell Specialized cycling shoes where the correct this in the shoe itself with a shaped insole, pain stopped over night.
We way to check this, and you'll look daft doing it, is to squat one legged with the other foot hooked behind, with your foot facing forward, squat down, if your knee continues to point directly forwards over the foot you are fine, if it turns out or inwards, this is what they need to correct.