I am having the exact same problem. I am on Windows 10, with ASUS bios v1401, but the same thing happened with Win 8 & v401 bios. When it trys to boot it can't find the SSD and goes to a black error screen. I reboot and hit F2 to come to the ASUS bios home page. There is a little window showing the drives and you are supposed to drag the icons to the proper order. Well, by SSD isn't shown, only the HD and the CD drives.
If I hit F8, I can see the SSD and boot from there, which at least lets me into my machine this one time.
Going to the Boot menu in the Advanced mode, I can't see any way to identify the drives or to adjust the boot order.
Any help would sure be appreciated.
Thanks.