lex,
I am three years into riding, and occassionally I have knee pain. Here's some suggestions I have heeded to cure the problem.

1.Adjusting the seat, not only up or down, but forward to back. I've had to scoot mine back to eliminate that sort of pain.
2.Hamstring strengthing workouts. Some home works outs could be.....get a couple of heavy cans of food, or free weights, one for each hand. Stand with feet shoulder width apart and back straight. Keeping legs and back straight. Bend forward at the waist, arms with weights extended toward the floor and reach as far as you can. Return to upright position and repeat. Do this at a moderate pace and repeat at least 20 times. Maybe even more than one set. Be careful not to fully lock out knees, this could be painful or cause injury.
3. Clipless pedals are the bomb girl, and they may help rather than hinder your problem. Right now you have a limited range of motion to pedal in. With clipless pedals you can pull across the bottom of the pedal stroke and up the back of it. This way you're using more muscle groups. You could just be over using that muscle group.
4. Relax into the pedals strokes. Don't mash them if you do not have to. Set a speed that's comfy and use the gears to keep it that way. If you are continually straining your legs through the entire ride, strain may show up as pain.

I hope some of this helps. I am no expert, but I've been around the block. Keep on riding girl.