There seems to be a bug on Apple's side that causes the iPod to periodically reboot back into the Apple Firmware while it's off. This happens often on my own iPod, usually when I leave it off overnight and come back to it in the morning. (Not to mention the fact that I click the hold switch on as I shut it off; force of habit.)
If you shut your iPod down from Rockbox and come back to it a few hours later, only to be greeted by the Apple firmware, just reset it (MENU+SELECT). Until Rockbox can be permanently flashed to the iPods, thereby eliminating all traces of the Apple firmware, this is the only thing we can really do.