I have used this part before in almost exactly the same configuration which was almost exactly copied from BBB.
What seems to happen is that is I let my system fully boot and then shut it down, the device goes in to some type of fault for 5-7 minutes before I can restart it from the pushbutton.
The only external indication I can find that is in this state is that the BYPASS pin which normally should be about 2.25 Volts, pops up to almost the battery voltage. When this signal drops back down I can start the system again