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I have an Intel® NUC Kit NUC6i3SYH Specifications with Windows 7 installed, and I have never experienced such behavior. Does the issue persists with a previous BIOS version? Try downgrading the current version, and try installing 044 one more time, follow the recovery method, see here for the instructions; BIOS Recovery Update Instructions for Intel® NUC.
There is something strange...
After installing the OS with all available drivers the System said there is an unknown device listed under USB Controller in the device manager (path 0 (port_#0007.Hub_#0001). This failure seems to block the system to load the USB 3.0 drivers until that failure is processed and therefore Windows 7 is not controlable by USB mouse or keyboard for about 12 seconds. So this problem causes the waiting time between "Windows 7 desktop appears (mouse doesn't work)" and '"Windows 7 ready (mouse working)".
Nevertheless i started the Windows update-procedure though the system wasn't running smooth in the hope that maybe some drivers provided by Microsoft would solve the unkown USB device problem. A few hours and some restarts later nothing changed. I went to bed and next morning after powering up the NUC again windows suddenly detected the Bluetooth unit and installed suitably drivers. And that although i've installed the Bluetooth drivers provided by Intel directly after Windows installation without any errors.
The correct detection and installation of these Bluetooth drivers seems to solve the whole startup procedure problem, the NUC now starts in about 20 seconds and all troubles seem gone.
But i wonder, how a device which doesn't work properly in Windows is able to delay the starting process of the BIOS? Could it be, that there is a HW-failure (maybe temperature-sensitive) regarding the Bluetooth unit? And now, as the Bluetooth unit seems to work properly (at least temporarily) both, the BIOS initialization and the Windows startup work well, independent from eachother but regarding originally to the same HW failure?
If you can't provide a better explanation than a HW failure I'm thinking about to replace that NUC unit, especially i'm within the legal replacement-time at the moment.
Many thanks, Flavius