Here is my short list of possible remedies:
1. Adjust the cables (I assume they're cable operated, opposed to hydraulic) if the levers are bottoming out against the handle bars.
2. Clean the rotors and pads with rubbing alcohol (oil, dirt a/effect performance).
3. Give them time to break in. The instructions that come with my Hayes disc brake pads recommend something like 25 good hard stops to develop the full capability of the pads. I assume this is similar to other brand pads, and considered a "break-in" period.