What Causes Pain In The Knees?

Hi my daughter is 15 for a few years now her knees will swell, get red and feel hot. she will sometimes be very stiff in the morning. She complains her ankles and wrists hurt. We have had her tested for JRA. It came back negative. We have since changed drs. Her new dr said she may have it because there are different types of RA. Can JRA cause left sided flank pain? My daughter has been having this pain since Oct along with hematuria at times.