I've had intermittent SATA issues with my current motherboard since almost forever. Sometimes it just won't boot, or (sometimes) even post if a hdd is connected. If I disconnect the drive, boot up with a cd (my go-to is
systemrescuecd, haven't really tried it with anything else), power down and reconnect the drive, it seems to reset the bios (or something) and then the pc can be booted with the drive connected, even if the hdd itself won't boot.