Knee problems on bikes are not unusual but in the main can be cured. Fit is the main thing with saddle position being very important. Cadence- or the speed you pedal at is another. Low RPM at the pedals with high gearing will put strain on them so another thing to look at. Exercise and training of the muscles round the knees (Called the quads). If you can improve the quads- then the knee takes less strain.