Hi Gelianna,
I tend to get pain near joints, but not in them. Usually muscle tissue or a tendon an inch or two away from the joint. I have had pain in my wrist, which I think is partially BFS, but I've been able to mostly resolve it by changing posture at the computer.
My knee has been bothering me quite a bit. The pain seems to be below the knee cap on the patellar tendon and occasionally around the knee cap. But not deep in the knee joint.
I don't know if this is similar to your knee problems?
I have had ankle pain where the ligaments cross over the top of the foot.
I know other are other members that have specifically mentioned joint pain.