Sounds like the BIOS isn't using AHCI but everything works with the OS AHCI driver is loaded.
Is the BIOS set to AHCI (but from your report, it seems like it is)? If not, it should be. If it is, what happens when you set it to RAID?
Also, try to boot with only the SSD connected one time (although I see you've already tried that).
On my own Frankensystem, it doesn't boot unless the BIOS is set to RAID, and I've not got the inclination to debug that.