The most common cause of knee pain in someone your age that occurs in the pattern you describe (aching pain when the knees are in the same position for a long time or with bending the knees) is called chondromalacia, patello-femoral pain syndrome, or 'runner's knee.'
In this condition what happens is that the cartilage in the knee cap (patella) between the big leg bone (femur) and knee cap begins to soften and break down because of poor tracking of the patella over the femur with knee bending. This leads in particular to pain with bending of the knees (such as while climbing stairs or when seated).
In addition to rest (for example, backing out on any running or other exercise routine), you should talk to your personal trainer or your primary care doctor
about some leg strengthening exercises. This is because strengthening the quadriceps can often help with patello femoral pain syndrome (of course avoiding exercises that involve bending the knee, which stresses the cartilage in the knee cap). Also, sometimes a more supportive pair of shoes that helps you to avoid overpronating the feet can be helpful in reducing stress on the knee cartilage.
I would set up an appointment with your primary care doctor to discuss the problem.