Are you balancing the battery?
It is possible for a single cell to be overcharged or over discharged preventing it from charging normally.
There are a couple of good lipo balancers for around the $25 price.
http://www3.towerhobbies.com/cgi-bin...&I=LXMRZ9&P=ML
http://www3.towerhobbies.com/cgi-bin...&I=LXMGS7&P=ML