Which device is used to boot from is specified by you in a setting in the BIOS Setup screens. Although the displays allow you to choose which hard drive you boot from, in fact they are really offering you the choice of which PORT you want to boot from, and using the current port device to identify them. So it appears your Boot Priority Sequence was set at a time when your bootable SATA drive was connected to SATA_3. If you changed it after that the BIOS will NOT look anywhere else for that drive unit - it will only look at whatever is connected to the SATA_3 port for a boot device.
So, as others have said, you could simply recreate the original conditions - put the bootable HDD on the SATA_3 port where it is expected, and connect any other HDD's to other ports. If you REALLY need to move that bootable HDD to another port, you will simply have to change the way the Boot Priority Sequence is set in BIOS.