When is a Shutdown not a Shutdown? When Windows 8's Fast Startup is left enabled.
This caught me out the other day despite having read about it a little while ago: clicking "Shutdown" in Windows 8 & 8.1 does not, by default, do a full shutdown. Instead it doesn't what's called a 'hybrid shutdown', which is roughly somewhere between shutdown and hibernate. Users are logged off and their processes are closed, but system processes stay in memory (i.e. all your background services) and the machine then goes into hibernate.
This caught me out when I'd asked someone to shutdown their computer and then power back on to troubleshoot. The problem didn't go away as expected, and the uptime reported by WMI was still reporting several days instead of the few minutes I was expecting.
Clicking "Restart" does do a full restart. Bear this in mind when phrasing your instructions to users when asking them to completely restart their computer.
More info: Fast Startup - Turn On or Off in Windows 8