Sometimes when I use the shutdown option in cinnamon the system closes some of the running programs and then just sits on the desktop until I tell it to shutdown again. The shutdown and poweroff commands never have this problem and with the shutdown option it only occurs rarely but primarily seems to occur if I shutdown during disk activity such as a download from steam. My system just started doing this when I did a reinstall of Linux Mint to switch from a BIOS emulated boot to a native UEFI boot. It's not a huge issue but I would like to be able to tell my system to shut down only once and have it do it. I've taken a look in syslog to see if there's anything weird around shutdowns but there doesn't seem to be. 
Linux Mint 17.1 shutdown option doesn't work
linux;linux mint;shutdown