Running on a treadmill will place large amounts of stress on yours legs due to the resistance giving that jarring effect on the leg muscles so as suggested i would try to avoid it until a time that your confident you knee pain has dissipated. As for the knee pain itself it could be several things but most common cause are poor running technique or inversion/eversion of the foot whilst running ... do you where orthodics ? could also be imbalances of the upper leg muscles surrounding the knee which is common in a lot of runners basically your vastus lateralis (the muscle on the outside of the leg) can tend to be stronger than the vastus medialis muscle (on the inside of the leg) which in effect can cause patella alignment issues of the knee and place additional strain on the ligaments causing pain according to the weaker side of the leg.

Either way i would run it past a physio and try get ontop of the pain side of your running straight away cause knees are horrible joints for injury and can lead to long term effects mate !