Let me get this straight.
You see the DVD Rom in Bios ->Then shutdown PC and plugged in the HD in the same SATA & power cable from DVD Rom -> Then booted and it showed no HD on Bios?
You shouldn't be able to see the DVD Rom drive as you're using its cables (sata & power) with no other peripherals connected to any ACHI ports.
No, I pull everything out including USB sticks and so on.
Plug in the DVD rom on a sata cable and boot the machine and it shows up in the BIOS, then shutdown and pull the DVD
I plug in the HD on that same cable and nothing, shutdown.
I put that DVD on the same cable as the HD was on and its back, shutdown, plug in a second (known to be working) sata cable and plug in a HD. Boot the system with a freenas 9.3 disc and nothing but the DVD shows up. Shutdown.
I plug in 9 HD's across the sata and sas controllers along with the DVD rom and boot the system, freenas shows up gets to the install prompt and I say yep install, no HD's available. Shutdown.
I plug in a USB stick along with 2 x 3TB WD reds, 4 x 2TB reds, 2 x 880GB greens and an old 150MB WD raptor and I boot, BIOS finds DVD and boots freenas, freenas finds USB "ONLY" nothing else shows up, finish install and boot freenas off the USB and it cannot see any HD's either.
I probably didn't explain myself to well before sorry about that.