I recently spend some time figuring out this problem and can confirm that - in my case - the following BIOS setting (I'm running BIOS 0030) fixes the problem of the drives not being detected by the operating system (Windows 7 in my case) upon startup:
Enter the BIOS -> Power -> Enable "Deep S4/S5".
Actually, settings this option solved all USB problems I had with my D54250WYKH NUC. Even the issue with the HDMI-CEC adapter from Pulse Eight, which didn't work after powering on my NUC. It now works fine.