Did you top off the master cylinder with fluid every 3-4 pedal strokes? If not, you were probably pumping air into the lines. As soon as the fluid level gets low in the master cylinder, you are running the risk of pumping air into the brake lines.
It sounds like you are doing it right, but just to be sure...
1) Top off the MC with fresh fluid.
2) Go to the farthest caliper from the MC (if you are bleeding the entire system, that would be RR, if just the fronts, that would be RF)
3) Crack the bleeder screw loose, but don't unscrew it. Attach short piece of 1/4" ID hose. I use a small bottle to collect the old fluid for disposal.
4) Have assistant push pedal (not too hard) and make sure they hold it down until you tell them otherwise.
5) While assistant is pushing the pedal, open the bleeder screw, allowing fluid to bleed out. When the pedal reaches the floor, fluid flow will stop. Screw the bleeder screw shut.
6) Once the bleeder is closed, say "UP" so your assistant knows to release the pedal.
7) Repeat 4-6 approximately four times. Check the MC fluid level. Top off if necessary. Repeat 4-6 another four times. Top off MC, move on to next caliper.
At least that's how I used to do it, before I installed SpeedBleeders. Also note that brake fluid absorbs moisture from the air fairly rapidly. Never leave the MC cap off for more than a minute or so, especially in humid weather.