Quoted from Coyote:
Interesting, I see two apparent 'batteries' - one molex plug named 'Battery', and one unpopulated 'BAT1'..
The BAT1 is for the real time clock for the Beaglebone Black interface. I built this board by hand and didn't have that part in stock. It will be populated in the released boards, of course.
The "Battery" connector allows a user who wants to use a Beaglebone Black the ability to have a "safe shutdown" of the Linux OS running on the Beaglebone Black. The FAST WPC Controller and FAST Core Controller both include this "safe shutdown" circuitry that when the 5v driving the board is cut, it switches to the power provided by a battery just long enough for the triggered "shutdown" of the Linux OS to complete its shutdown process.