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Seamless shutdown with PC power button

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My cabinet runs Windows 7 with a HyperSpin shell (via Instant Sheller). I've wired my motherboard's power switch to a button outside my cabinet, and there are two ways that I can shut down my system:

Method #1: Quit HyperSpin

When I quit HyperSpin, I run a batch file that waits a few seconds and then sends a shutdown command to Windows. I added the delay because HyperSpin doesn't always close right away, which results in a message about how HyperSpin needs to close before Windows can shut down.

Method #2: Hit the power switch

Windows shuts down when the power button is pressed. However, 50% of the time, I get the message about how HyperSpin still needs to close.

I could add the AutoEndTasks registry key to force a shutdown, but I'm concerned that this could corrupt my HyperSpin files. Is there a better way to avoid the "Programs still need to close" message when I hit the power switch?

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Force Shutdown
To perform a Force Shutdown, type in Shutdown –s –f. Notice a new parameter –f? This parameter is responsible for Fore Shutdown.

Force Shutdown with Time
To perform a Timed Force Shutdown, type in Shutdown –s –f –t 00. This will Force Shutdown your PC in 00 seconds (waiting time). Setting it to 05 will shutdown your PC after 05 seconds i.e after waiting for 5 seconds.

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