I have ran into a similar issue.  My Lenovo Flex 15-2 is currently running 
Debian Jessie amd64 Stable Release.  When I issue the shutdown command either 
via the menus in gnome or gym, it goes through the process of shutting down and 
powers off.  Approximately 5 seconds later, the laptop powers back up and 
continues with the booting process via grub.  Mind you the computer has not 
been touched since issuing the shutdown command.  The only way I have been able 
to get the laptop to shutdown and power down successfully is by having a USB 
mouse connected.  I’m thinking that the installation has some corrupted files 
and I am thinking that I just need to do a clean wipe and reinstall, but I’m 
hoping that it’s something much simpler.  I ask for advice to which direction 
to go as I am a novice.

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