So let me get this straight :
Battery ran out device shut down
Charged device and turned on
Ran Pangu , locked screen , received notification ...... And basically it crashed , failed to boot into non JB state or failed to boot to JB state ?
Sounds to me like you're timing is a little out !
Turn off device , now turn it back on ...
Open Pangu app and count to 20 don't tap nothing just open the app and count to 20.
When you have counted to 20 , tap the big circle and again count to 20 , don't tap nothing just count to 20.
Now lock the screen wait for notification , device will respring and should be Jailbroken again.