There are two small bones, called the sesamoids, under the main joint of the big toe. Inflammation of the tissues around the sesamoids is called sesamoiditis. Sesamoid problems are common among runners and other athletes who do similar movements of the big toe.
It is concerning that your toe pain got worse after adding more miles, and that you still have pain even after rest periods. You may have developed a stress fracture in one or both sesamoids. You should see your doctor.