i recently upgraded my mobo cpu etc and did a clean install of windows vista 64, whenever it boots up on the black screen it looks like it goes through the checks and then says no hard disk has been detected? yet it still boots and everything seems normal and in the BIOS its there and on my computer its there. i also installed a new optical drive, they are both SATA and on the mobo connected to the 3gbs port. the optical drive seems fine.
Could be that Sata or Power cable might be a bit off, make sure that they are securely attached. Also you might have the drives reversed on your motherboard.
(check that HD is on (0) and DVD is on (1) and not viceversa.
verify then that they appear like this on your Bios.