Manual Shutdown After Shutting Down Normally

Sometimes when I shutdown with letting the timer run out, an error message pops up saying that I need to shutdown manually and restart. After booting up, I report the error message to apple and the title is along the lines of ... you did manual shutdown because of a problem.
Does this happen to anyone else? Is this reason for serious concern?

so i quit all programs before i shutdown and then i just wait for the shutdown timer to run out.
I got my mac pro 9/8/09 and installed snow leopard the following night. This error message occurred noticeably when i first got the laptop and between now and then it was only occasional. Now its pretty much everyday.
it's like a game of chance with my laptop.. i never know what causes the error

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