You may have the same problem as Deep... have you configured the SSD as a single "Raid 0" array in the raid controller configuration?
The live USB may have the raid controller drivers installed by default, which would explain why you can see the SSD with that but not otherwise.
I wasn't using the raid controller as such, just set to ahci mode via bios which removes visibility of the raid.
You can't boot from the onboard SATA port in certain cofigurations. I run Ubuntu Server and just bought a PCI-E SATA expansion card which I can select in the BIOS to boot from via one SSD which cost me about £18.
Got a part number for the one you used? I'm considering this (eventually at least) as I'm going to have to stick more drives in eventually.
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