I have patelofemoral pain syndrome. is it normal that some nights my knees feel uncomfortable (not really painful) in bed so i can't keep them still?

Possibly: One of the things that can occur in patellafemoral syndrome is the development of arthritis on the undersurface of the patella. In general, patients with arthritis do have more pain and stiffness when the joint is immobile. The other possibility is that you also have another condition such as restless leg syndrome. Consider being checked. Thank you.

Often chondromalacia: The kneecap(patella) has cartilage like all bone in joints. If the patella is not well aligned , it may begin to wear and produce pain. This may require a trip to an orthopedist and a special x-ray known as a "merchant view". (named after the doc that described how to take it. It is not a simple retro-patellar view.