HI!
I have a D54250WYK and the similar problem. Even when I shut down the NUC completely, the connected USB 3.0 HDD (WD 3TB green) stays on and never goes in to the standby mode.
The Bios (0032) and the USB3.0 driver are up to date. Win8.1 is installed.
The second major problem is, when the external USB 3.0 HDD is connected the NUC D54250WYK will not start anymore. The screen freezes before I can enter the UEFI. When I disconnect the USB 3.0 HDD the start procedure resumes normally!