have you tried hooking up the windows 7 drive to sata 1 and/or sata 2 to see if it boot fine. If it does then the sata ports are working. Let me know the status on that then we can go from there.
Also check the following. Go into the bios and go to advanced. Open IDE Function Setup. make sure Sata Port 1,2 is enable and Sata Port 3,4 are enabled.