I removed calipers to paint them. When I replaced them on the car, I can not get the brakes to work. I flushed and bled the system from each corner. The brakes work after pumping the pedal 2 or 3 times then after a second they do not work again.
Any chance you switched them side-to-side? That will put the bleeder screws on the bottom where the air won't bleed out. At any point when you had to pump the pedal to work the pistons back out or when you were bleeding, did you press the pedal more than half way to the floor? That is a common way to damage the master cylinder, although what you're describing isn't exactly the common symptom. If you hold varying pressure on the pedal, it will typically slowly start to sink to the floor if a seal has been torn and is leaking internally.