A common question often asked is can Flat feet cause knee pain? The answer is yes and no. The fact is flat feet will not tear your mensicus or ACL, or cause arthritis. But flat feet can aggravate conditions of pain in the knee, mainly arthritis. But the fact is if you cure your flat feet there is still a very good chance that the knee pain will still be present. The best cure for Flat feet when you have knee pain is orthotics such as the ones here:
But no, your knee pain is probably not caused by your flat feet but maybe aggravated from it. When in doubt see your local Podiatrist with questions.