just wondering in your bios are all your sata ports enabled. I know from my bios I can disable specific sata ports even though it will display what is hooked to it.
have you tried disconnecting your new drive and see if the ssd boots the computer still as you say it has windows installed on it still?
are your drivers up to date on your new install? you might need to update drivers on your new drive so that all the sata ports work (im talking specifically about motherboard drivers/manufacture drivers)