hi

the baker´s cyste is a possibility concerning to the decrease in knee flexion. has the patient a feeling of pressure or "blocking" when he flexes the knee?
But also the popliteus muscle might be a reason for the pain. try to rotate the tibia at 90 deg od fexion (both internal and external) and fully flex the knee with the rotation. If pain increases/decreases it might be a sign of muscular problem. also the posterior horn of the menisci might be affected, the popliteus muscle attaches partly to the post. horn of the lat. menisci and pulls it backwards in full knee flexion. After ACL reconstruction often the small muscles are weak and their function is iritated.
ok good luck