FWIW, I've been having what sounds like a similar knee pain. In my case it's both knees (although usually not equally), under the knee cap. From some internet research it sounded to me like it's what's called runner's knee, which comes from the knee cap not tracking properly over the bits underneath it. (can you tell I'm not a doctor?)
If that IS what it is, I found two solutions, which you might use in tandem.
1) adjusting your bike setup/foot positioning (as suggested above)
2) doing exercises to help balance out the muscles surrounding your knee. Say, the muscles on the right side of your right leg are a little stronger than the inside and they pull the knee cap a bit out of line as you pedal.
I don't know what those exercises are yet, and I'm going to be seeing an orthopedist in a week or so just to make sure because my knees are dear to me.