1. Are you saying that when the SSD boot drive is the ONLY drive installed the system boots and functions problem-free?
2. So it's ONLY when the HDD is installed as a secondary drive that the SSD is not "recognized", right?
3. What exactly happens? What kind of a message do you get about the system not recognizing the SSD?
4. Since you indicate the HDD has been added to the system we'll assume the HDD was NOT the original boot drive whose contents you cloned to the SSD so that the latter disk could function as the boot drive in the system? That's right, isn't it?
5. The HDD is new? Have you tested the HDD with a diagnostic program preferably from the drive's manufacturer?
6. You've checked & double-checked to determine the SATA...