AFAIK Windows numbers the NICs (like Linux) according to the PCI addresses. This is displayed in the device manager under "Location", e.g.:
PCI Slot 192 (PCI bus 11, device 0, function 0)
Can you compare the PCI address information in the VM(T)X files between your template and a couple of deployed VMs?
I only have one NIC but things looks like this here:
# grep -i 'ethernet[0-9]\.pci' /vmfs/volumes/Datastore2/TemplateW2K8/TemplateW2K8.vmtx | sort
ethernet0.pciSlotNumber = "192"
# grep -i 'ethernet[0-9]\.pci' /vmfs/volumes/Datastore1/SomeVM99/SomeVM99.vmx | sort
ethernet0.pciSlotNumber = "192"
# grep -i 'pci' /vmfs/volumes/Datastore2/TemplateW2K8/TemplateW2K8.vmtx | sort
ethernet0.pciSlotNumber = "192"
pciBridge0.pciSlotNumber = "17"
pciBridge0.present = "true"
pciBridge4.functions = "8"
pciBridge4.pciSlotNumber = "21"
pciBridge4.present = "true"
pciBridge4.virtualDev = "pcieRootPort"
pciBridge5.functions = "8"
pciBridge5.pciSlotNumber = "22"
pciBridge5.present = "true"
pciBridge5.virtualDev = "pcieRootPort"
pciBridge6.functions = "8"
pciBridge6.pciSlotNumber = "23"
pciBridge6.present = "true"
pciBridge6.virtualDev = "pcieRootPort"
pciBridge7.functions = "8"
pciBridge7.pciSlotNumber = "24"
pciBridge7.present = "true"
pciBridge7.virtualDev = "pcieRootPort"
scsi0.pciSlotNumber = "160"
vmci0.pciSlotNumber = "32"
# grep -i pci /vmfs/volumes/Datastore1/SomeVM99/SomeVM99.vmx | sort
ethernet0.pciSlotNumber = "192"
pciBridge0.pciSlotNumber = "17"
pciBridge0.present = "true"
pciBridge4.functions = "8"
pciBridge4.pciSlotNumber = "21"
pciBridge4.present = "true"
pciBridge4.virtualDev = "pcieRootPort"
pciBridge5.functions = "8"
pciBridge5.pciSlotNumber = "22"
pciBridge5.present = "true"
pciBridge5.virtualDev = "pcieRootPort"
pciBridge6.functions = "8"
pciBridge6.pciSlotNumber = "23"
pciBridge6.present = "true"
pciBridge6.virtualDev = "pcieRootPort"
pciBridge7.functions = "8"
pciBridge7.pciSlotNumber = "24"
pciBridge7.present = "true"
pciBridge7.virtualDev = "pcieRootPort"
scsi0.pciSlotNumber = "160"
vmci0.pciSlotNumber = "32"
Note in my example:
pciBridge0.pciSlotNumber = "17"
Could correspond to "PCI bus 11" displayed in the Windows device properties (11 in hex = 17 decimal).