Who knows. You probably just need to do the power down, unplug for 30 seconds, and it should reappear. It's obviously just a glitch.
Remember they're not skins they're different versions of the gun. So when you're setting up your class and selecting the weapon you need to go to the weapon you want and select the MKII version of that weapon, not the base version it self. On Xbox you hit up on the dpad when you're on the weapon. Not sure on PC if you have that but I'd imagine its just and up arrow you'd click or something easy like that.