I don't know how to solve the issue of having the same BIOS UUIDs on multiple machines in this case.
But to make the 1000v use different IDs you could try to add something like
vemset card uuid [new-uuid]
to the local boot script of ESXi. See this KB article:
VMware KB: Modifying the rc.local or local.sh file in ESX/ESXi to execute commands while booting
- Andreas