Go back to a very basic system (with no cards installed) and only THEN perform the BIOS update. This sounds like a boot memory footprint issue (where there isn't enough memory left in the right 'space' to allow the bootable devices you're plugging in to work properly. Hopefully a new BIOS version (and possibly new firmware on the RAID card) will address it. You could alway try another/different optical drive or check to see if there's a firmware update for that as well.
If you have (U)EFI option in MB BIOS, try to disable it, it is common cause for bootable devices inaccessibility.