Ever since I upgraded to Windows 8.1 via the in-store update my PC takes a good 3-4 minutes to boot!!! I am on a GA-X79-UD3 + i7-3820 + Samsung SSD 840 for system drive. I have updated all my drivers to Windows 8.1 compatible ones and still. I have checked via Samsung Magician and the drive is using AHCI mode on (Intel PCH) Sata 3 6Gb/s. I have tried restoring my UEFI to default settings and enabling Fast Boot but still?? On Windows 8 it would boot in 5 seconds....
EDIT: Have tried Safe Boot and Clean Boot, still same
EDIT2: Will any Microsoft guy chime in?
Intersting, I have a Samsung 840 and a GA-H87M-D3H motherrboard and have the same issue and have followed the same steps.
First, I do not think MS believes this is their problem.
Second, as has been successful to myself and others, try disabling the Bluetooth driver(s) to see if that gets everything to normal speed.