"Off" is not entirely off on PocketBeagle

I have a little power problem with the PocketBeagle. It seems that when you use PB to shut the system down, it is not entirely off like when you apply power but before you push PB. All the LEDs on the PB are off, but Vout appears to still have voltage, and a number of I/O pins (like the one I use to externally show power is on) retain some voltage. I’m not really sure how PB actually works. What does the OS do vs firmware in the power control IC? Is there a way to programmatically force the PB into the same state it is in when power is applied but before PB is pressed?

For posterity, apparently because of an external hardware problem, the shutdown script was not completing before turning the processor off. I received no messages on the console, and I assumed when the BB Power LED was off everything was complete. So, the LDOs and everything do turn off if the shutdown happens as it should.