Patella femoral syndrome or maltracking of the knee is the most common presentation of knee pain where the outside structures of the knee are stronger than the inside structures of the knee. This causes maltracking and the knee cap to not sit correctly on the cartilaginous groove which causes inflammation and pain.
Often these people will get worse when sitting for long periods like on a long drive, a long haul flight, on a bike with the knee too low or when watching a long movie. This is because the knee is in a closed packed position where the knee cap or patella is closely packed into the groove on the femur which causes more inflammation and pain. This is rather than when you are upright where there is not as much pressure on the groove.
The first step is to consult your Physio Pro to discuss the causative factors for maltracking and patella femoral malalignment and the second step is to avoid the closed packed position in the short term until your biomechanics have improved.
This includes not doing hill or step running for fitness, lifting the bike seat up, frequent breaks with long sitting and bending and extending the knee when you have to sit for long periods.