A real full shutdown *should* cut power to all USB ports.

Don't confuse any of the "sleep" or other categories as being the full powerdown, though. For example, the "powerdown" of merely shutting a laptop won't cut power to the ports.

Sometimes there is residual current left in the power supply capacitors of residual components that are connected to USB ports, which can provide enough power to keep LEDs lit for quite some time, even though there is really no real power enough from that to actually operate the device. To find that out, leave it powered down for a longer time and come back and observe whether of not the LED has gone out.

--Mac

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