Sometimes batteries can go into protected mode due to a communication error on a low level software layer.In this case, Windows will recognize the battery and its capacity, but will not realize it is not giving power to the device. As a result, the device will never warn for low battery level but can at one point just turn off unexpected.
If you experience problems with your batteries, there is an easy way how you manually can check if they are inserted properly and communicating correctly: on the back of the batteries is a capacity indicator. Press it when you put them in and press it again after 30 mins. The capacity of both batteries should decrease evenly. If one battery's capacity does not go down as much as the other one, take that one out and re-insert it again to establish the communication between the battery and the device.
Should your device have turned off due to battery miscommunication and not turn on again, you can perform a power reset to release the lock state of the capacitors by taking out the batteries and mains and pressing the power button 10 times. Then, plug in the power cable again, turn on your device and charge the batteries until they are completely charged.
TobiiDynavox released a battery monitor to help you monitor the battery communication, if you don't have it already, you can update the C-Series Hardware Options to version 1.6.1 or later.