I had this problem too and just resolved it. For some weird reason, the ASUS BIOS only lets you use one drive in the Boot Priority list, but you can pick which drive that is. In my case, it had picked the drive I don't want to boot from by default, so I could only use that in the Boot Priority list. I could see the drive I wanted to use everywhere else in the BIOS, so it's recognized, but not in Boot Priority. It drove my crazy.
To change the Hard Disk to be used for Boot Priority, go to the Boot / Hard Disk menu instead. This cryptic menu lists all of your hard disks in a numbered order. Make your boot drive is the first one in the list (select #1, press Enter and pick your HDD) and go back to the Boot Priority menu. Now you should be...