The computer on my desk cannot boot from USB at all (because it is too old). Yours seem to boot from USB when no AHCI devices are attached; but otherwise fails to boot from USB and wants to boot from SATA only, right?
I found a few people on the Internet with this symptom; some of them fixed the issue one way or another, others--gave up. Good luck!
With six extra SATA ports you can go SATA only and just write off USB devices. That will make a more resilient system anyway.
That is what I am thinking, just take one of the ssds and install to it, the other for the zil, 3rd for l2arc. I will take the ssd and an install stick to work to creat the boot device.