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The first time, -t sec tells the init process how many seconds to wait before sending processes SIGTERM or SIGKILL -- time for those processes to end themselves before init does it by force -- and changing runlevel.
The second time, delay names an interval between typing the command and actual activation of the shutdown processing. The documentation says,
"The time argument can have different formats. First, it can be an absolute time in the format hh:mm, in which hh is the hour (1 or 2 digits) and mm is the minute of the hour (in two digits). Second, it can be in the format +m, in which m is the number of minutes to wait. The word now is an alias for +0.
If shutdown is called with a delay, it creates the advisory file /etc/nologin which causes programs such as login(1) to not allow new user logins. Shutdown removes this file if it is stopped before it can signal init (i.e. it is cancelled or something goes wrong). It also removes it before calling init to change the runlevel."
There used to be a resource file or similar that shutdown would read for system-wide default delays and such. That no longer seems to be available as of Ubuntu Jaunty and similar distributions.