What could cause a menstrual cycle to stop after 3 days, then restart two days later?

Low progesterone. For women with irregular menstrual cycles, problems with ovulation are usually the cause. When you ovulate strongly, you produce progesterone which peaks and then falls. Once the progesterone gets low enough, you have your menses. If you produce low or very low amounts of progesterone, your menses can stop and start irregularly. If it only happens one time then not much to worry about.