Eventually, small amounts of stress are placed on the unsupported joint. After enough time, the body is intelligent enough to lay down calcium over the affected area. This is a protective mechanism by your body to try and reinforce a weakened area. It sounds like you haven't reached that state yet. I would advise you to find a well trained chiropractor, or sports physician, to check the alignment of your pelvis and knee joint.
Many chiropractors practice sports medicine.
Ask your friends or family members about someone thay can recommend in your area. Find one that can explain your problem and also explain the treatment options. Your pelvis should be easy to clear up. I would guess that your baker's cyst is going to be caused by a group of weakened knee joint muscles. The lack of muscle support allows for the bones that make up the joint to shift abnormally.