Are you using DOT 3, 3-4, or 5?
With DOT 5 I have had problems before. Especially when by myself. One thing I do is step on the pedal hard for about 3-4 times, then barely depress the pedal and "mini pump" it or tickle it right when the bubbles come out of the master cylinder. Repeat that over and over again and it might slowly pump up.
I'm sure you already know this but, never let the master cylinder get empty or you will get more air in the system.
