Sooooo, couple of months later. Microsoft premier support could not find anything wrong with our 2 DCs, one physical one virtual.
When I shutdown the virtual DC - the problem is gone! There are no more duplicate entries on the 3.0 subnet.
They had both running the DHCP Role. Three days ago I uninstalled the DHCP role from the DC VM and the problem is still present so that leaves us with the conclusion that the DNSes are having somekind of a "misfire". I will completely demote the DC VM and create a new one without the DHCP role, just AD and dns.
Cheers!