The batteries really don’t power anything unless ground power or on board generator power is not available. They are back-up/auxiliary power only.
“In the case of the 787, two 32-volt lithium-ion primary batteries provide power as key elements of the aircraft’s more-electric architecture. The main battery, located forward in the electric/electronic (E/E) equipment bay below the cabin floor by the front passenger doors, provides power for aircraft start-up, ground operations such as refueling and towing, and acts as backup power for the electrically actuated brake system. It can also assist the second battery, located in the aft E/E bay, in starting up the auxiliary power unit (APU) and, in the event of a power failure, energizes essential flight instruments in the flight deck until the drop-down ram air turbine spools up.
The battery that caught fire on the Japan Airlines 787 in Boston was the second main battery. This unit’s primary purpose is to electrically start the APU when neither of the engines is running and the aircraft is not connected to external ground power. In this case, the battery energizes the righthand of the two starter/generators connected to the APU. The aft battery also provides another minor role, namely to power navigation lights during battery-only towing operations.”
http://www.aviationweek.com/Article.aspx?id=/article-xml/AW_01_21_2013_p22-537845.xml
So in short this was a starter battery (and a backup breaking battery) - if I read correctly. Sounds like the load for starting is greater than the battery is designed for - if after starting the engines, it has to come into play too soon afterward for breaking. Too much demand for too small a battery perhaps?