This is a question I get asked all the time. A ‘normal’ scan can be a real relief, but then be met with the mixed emotions associated with unexplained pain.
It is extremely common for patients with patellofemoral pain syndrome, (PFPS) to have a normal scan, and this is because the pain is usually driven by poor mechanics, and not poor structure. In other words, you can have an entirely normal knee form a structural perspective that can still be causing pain as the mechanics are not correct.
If we think about the anatomy of the kneecap joint, (PFJ) this is more easily understood. The knee cap is a floating piece of bone that is held in place by soft tissues, including several muscles. If these are too tight/weak/overactive or underactive this may pull the knee cap in to a strange position. Furthermore the groove that the knee cap sits in is the end of the thigh bone. Therefore, if the thigh bone drops in slightly, the groove will spin away from the knee cap.
When the knee cap and thigh bone are aligned well, the pressure is spread across a larger surface area, and hence the pressure per cm squared is lower. However, with relatively small changes in the position of the knee cap, thigh bone or both, the pressure will dramatically increase, and can lead to pain. This is also explains why your knee might hurt sometimes and not others, (for more on this see my blog on why does my knee hurt sometimes, and not others.)