I’ve been looking into this, and have spoken to one of our MCT instructors.
The machines I was imaging were Server 2012 R2, with Hyper-v. The Macs were duplicated on all the images. The instructor pointed out that Hyper-v moves the original Mac into software and uses the physical card as a glorified pass through device, so in effect the physical Mac becomes software, which explains how the situation arose.
I hope this helps anyone else imaging 2012 R2 Servers.
Could you mark this as solved and edit the title to “Nasty Problem - Fixed, Don’t get caught out when imaging Hyper-V Hosts”