prolly a bedding/break-in issue
You can try re-bedding the pads.
Basically, do this
1) remove the wheel
2) remove the brake pads, and remember which one was the inside and outside pad. I scratch an I and O in the back with a screwdriver.
3) lightly sand down the pad with 100 grit or so sandpaper. Clean with brake cleaner from the auto store or rubbing alcahol and a clean rag (not oily). Put them aside to dry.
4) take a clean piece of 100 grit (or so) sandpaper and make light swirly scratches around the brake track surface of the rotor. You don't have to go nuts, but try to cloud them up reasonably well. Scratches going radially across the rotor, rather than with the rotor will work better. Clean the rotor with brake cleaner or rubbing alcahol and a clean rag.
5) put it all back together.
Your brakes will suck for a while until the pads break into the rotor a bit. A bunch of hard stops should do it. I even ride my bike around the block in low gear while dragging the brakes one at a time.
Works for me.