First, when using a vacuum bleeder you need to put teflon tape around the bleeder screw threads or you'll suck lots of air in making it look like you've got air in your lines.

Second, when you pumped up the brakes I hope you did it slow and gently. Stomping the brakes could foam the fluid if you had air and could have also activated the valve in the distribution block that will close one circuit if pressure is much lower on that circuit. It also causes your brake light to come on. These will sometimes reset if left alone over night.