The WD AlignTool could not detect the AF drive

The AlignTool could only detect the first drive, which is an non-AF Caviar Blue, but it could not detect the WD20EARS, which is used for data storge. Is any problems occurred?

Thanks.

Did you tried using the boot CD? Do you have the hard drives connected directly to the motherboard or using and external case?

I did not use boot CD, the AF drive is attached on the second SATA port.