Hmm.

You might try formatting the new one. If it is formatted incorrectly, Windows will not pick it up. Usually the factory NTFS formats are good, but not always. Now why you would see it on the old system and not alone, I don't know.

Also, you might try mirroring to the new drive just to see if the Windows installer picks it up when it is alone. If it does, you can just install over what is there. You have a backup, so if it does not work, no big deal.