Hi,
My 6 yr old daughter wakes up with knee pain often and has for a few years now. Our CF team says it is common but they don't know why it happens. In her file they have indicated "cf related arthritis". We notice it more when she is tired due to a long day or lack of sleep.
If we catch it as it starts to hurt then a warm bath or heat will help, otherwise when it is really hurting (to tears) we give her tylenol or motrin. It will actually wake her from a sound sleep.