I used to have a similar problem where after uploading anything to the
disk via USB I would have to power cycle the battery after disconnecting
the USB. But that was with an older version of the code.
Never had that happen after uploading or removing music/files with either the USB or Cradle.
This issues seems to happen when it is in the cradle (2nd cradle) playing music through my stereo. Which is some thing I've been doing since day one. I have a funny feeling it is this latest version that is causes this, as this began just after updating it. May just go back the the previous main version and see if this condition goes away or not.
UPDATE: Seems to not be shutting down after all, but instead it is locking up. It happened again today so I pulled the unit out of the cradle. After which I held it to my ear and I could hear the drive still spinning. I'll down grade back to the older Rockbox and see if that cures this problem.