For a healthy mid-twenties man that lifts weights & runs and eats right can knee pain (w/o wts for 3 months) be caused by flat feet, over-walking?

Knee Pain: The biomechanics of the foot has a big impact on the ankle, knees, and hips. Flat feet over time can lead to pain in the knees specially if you are very active or on your feet a lot. You may need to see a Podiatrist to get custom orthotics to help align the feet and reduce stress on the knee.

Possibly...: But instead of guessing and assuming, see your doctor for a thorough evaluation of your knees. Only by doing so will you be able to arrive at a specific, addressable cause of your symptoms.