If the knee pain is toward the outside of the knee your illialtibial band may have tightened up from this new repetitive use from cycling.When tight it rubs along a bony protusion on he outside of the knee joint causing inflamation of the band sheath.

The cure is stretching: while on your back with legs extended flat grab your foot and pull your sore leg across and over your other leg toward your chest pulling gently;you should feel the band pull along the outside of your knee up to your buttock. Holding this position and genty increasing your pulling pressure for several minutes has taken care of this problem on many a tour for me. I hope that it works for you if that is the problem.
As noted above seat position up/down front/back are very important; also your foot position on the pedals using cleats or toe clips should be with the ball of your foot over the pedal axle.