360 controller light flashes when computer is turned off

I assume you mean a wired controller since you say 'unplug it'. I will test this out.

I would, if I could find my wired controller :/
 
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Anyone know how to stop this without unplugging the controller? It's a stupid feature.

Click the battery compartment open then close it if it's a wireless. Or plug it into a usb port that does not have constant power even when PC is off. <--- If it's wired
 
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You can configure if the ports on my asus mobo have power on power down or not - have a check of your manuals.
 
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