Don't know about earlier Windows versions, but newer server operating systems might indeed have a problem with that (at least if the disks also have the same size). You might have to override it in diskpart or something. The difference is that the drives should both show up, but one is marked as "offline".
The drive isn't seen in diskpart or Disk Managment it's flagged in Device Manager under other devices.
How about generating a serial number on the fly from, say, a hash of the creation date of the CHD (if that's stored somewhere?)