I installed Loki fresh from a usb stick. I replaced the graphics card and had some trouble (see this question) After fixing this, the bootup process takes an extremely long time.
Bootup with the AMD card was fast.
Bootup with no graphics card is fast.
Bootup with Nvidia card is slow. Before, time from reboot button to login screen was < 1 minute. Now it spends at least that long on the motherboard splash screen. Let me know if I can provide more info.