I have D945GCNL motherboard. I have used 80 GB,120 GB,160 GB, 500 GB hard disk's with this board and i didn't have any flaws. I had 2 * 500 GB hard disks also and it was working fine. So please check the hard drive. Try running the Seatools utility from Segate to check if your hard disk is good.
1. Check the following: Connect sata drive to sata port (ICH7) and ide drive to ide port of your board.
2. Bios must be properly set to reflect the drives.