We had someone the other day that came to the conclusion the bios had been messed up on his system. It is hard for me to believe installing an OS or just about anything else would mess up a bios. If the system booted to the flash drive normally, earlier it should boot to it again if that is the only available device.
If you have booted the Flash Drive as UEFI, it would not have given you the error message. But on a UEFI install, there are four partitions considered critical. In order to install over that OS without doing an upgrade you would need to remove the prior partitions during the install process. Data partitions should have been fine, unless you were actually changing the configuration of the hard drive.
But just in case, do you have a way to re-flash the bios on that system? I suppose some systems, usually laptops, do not actually let you into the bios but offer a setting utility in its place. I suppose that could be corrupted but even that should not effect your Bios.
You may end up needing Factory Reset media from ASUS.
On a side note, I suppose a CTRL-A also has no effect during boot. If the system was using the Intel Smart Response Technology, you may have seen the RAID configuration utility during boot.