If the HardDrives are new, you will need to use an ATA ribbon cable that has 80 connectors. This should have come with the new drives. Don't use older cables laying around, unless your certain they are 80 pin connector cables. The older ones are 40 pins, and will not give you the transfer rate the hard drive supports.
It is possible, but unlikely, that the cable is installed reversed. Make sure you have the cables hooked up correctly.
Also did you format these new drives? You may have to format them before using.
If your getting a CMOS error, it can be related to the incorrect hard drive settings. The battery CAN also be dead, just because the system is new, does not mean the battery is. The battery could have come from inventory that was stockpiled for an incredibly long time.