1. Third party apps may not be accurate.
Occasionally, the battery may not show a full charge (100%) in OS X, even after the power adapter has been connected for an extended period of time. The battery may appear to stop charging between 93 percent and 99 percent. This behavior is normal and will help to prolong the overall life of the battery.
3.If your portable Mac has a built-in battery, you don’t need to calibrate the battery.
4. Reset SMC. http://support.apple.com/kb/HT3964
Choose the method for:
"Resetting SMC on portables with a battery you should not remove on your own".