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I tried to replicate your issue in my lab but I didn’t get any problem. Please update the BIOS of the NUC using the recovery option. It is necessary to download the BIOS version 0353 .BIO file; remove BIOS jumper.
Then, restore the BIOS jumper, turn the NUC on and get into the BIOS, reset settings with F9 and save changes with F10. Restart the NUC and double check if USB S4/S5 Power option is disable. Keep the rest of the settings as default.
Devices plugged to Orange USB port will have power always even if the NUC is off. The option Portable Devices Charging Mode at Devices tab, gives the opportunity to change when the USB port provides with more energy. This port will be active always.
Thanks for the response. Meanwhile I did a recovery downgrade to 0249 and upgrade to 0353. Then I noticed that it *does* work when the system is shut down from the OS (in my case Linux, but I also tried Win 8.1 on a USB stick). I first noticed this issue (and did subsequent tests) by pressing the power button while in the grub (bootloader) menu. So: USB power is properly removed on OS shutdown but not if shutdown via a short click on the power button (while in some non-ACPI "OS").
My question is probably answered in that this is not a hardware defect, but may be a software / BIOS issue.