This may sound nuts , but it might be your trouble , WD erase doesn't really erase all the data on a drive just the boot partition , I think.
Like Blain I use Active@ Products if you use Blains link on that site you will find a program called Kill Disk if you use it it will wipe your drives by writing zeros to every sector on the drive.
I do this to get clean install for OS, If your not installing OS the disk tools in your OS or Active Hard Disk Monitor are just fine.
What MB do you have ? Do you have data on one drive and none on the other ? This can skew your results awww doesnt matter if you use kill disk, if you run disk tools in windows you are begging for trouble unless you are formating a new drive. I dont run anything more than defrag or Format in windows and its unwise to try anything that can affect your primary drive with your OS on it.