I was thinking the Fast Boot options in BIOS under, Settings/ Advanced/ Windows 8 Configuration/...
But seams like "MSI FastBoot" should allso disable PS2 device.
And if you use normal Fastboot you should have needed to disable USB device your self atleast on my MSI Z87-GD65 Gameing MB BIOS in default they arent.
So check how those are set on your MB, to be sure.
Heres an picture of my BIOS. If i enable Fastboot i still need to diasble my device one by one.Edit
: hmm wait, if MSI Z87-G45 had that "MSI Fast Boot" -option then how you get in BIOS ?
1: Clearing CMOS yeah, but i would think then on that Board it dont disable ps2. Because otherwise you would need to save your settings in profile to get fast past setting all little things up..