The method I use to shut down my box is as follows :

shutdown +3 -h

logout

the box indicates shutdown complete, so I switch off the power. When I reboot next time I get a Warning message in the bootup screen stating the that it was not shutdown correctly. being a newbie I'm kind of hoping for the correct method to stop these messages.

the final message should be something like
"system halted"

i am not sure how much of a difference it makes, but shutdown wants the argument first, then time, ie:
shutdown -h +4

however if you use -t to specify amount of seconds until shutdown, then -t comes before desired action, -h.

try it with -h first.
shutdown -h +3