Are you guys sysprepping the OS prior to converting the VM to template? I ask as I have found that this seems to be what is breaking the VM customization for 2012/2012 R2 VMs. If I don't sysprep the OS prior to converting to template, the VM customization runs as expected.
If I sysprep the OS prior to converting to template, when the VM customization runs, the following WMI query gets run and bombs out, which seems to cause the whole process to fail.
From the C:\Windows\TEMP\vmware-imc\guestcust.log
select * from win32_networkadapter where Manufacturer != 'Microsoft' and ServiceName != 'VMnetAdapter' and manufacturer is not null and MACAddress is not null
Found 0 objects. Pointer 0. return code -2147217398(0x8004100a)
After this, each reboot leads to a message on screen saying VM customization in progress. The only way to get rid of it is to follow another VM KB article for an entirely different issue, but same symptom, which requires removing something from the registry.
This seems to coincide with some of the other posts above about uninstalling/disabling the network as being a potential fix. The WMI query above seems to query the network adapters of the system. It seems this runs while the OS is still trying to finish the previous SYSPREP putting the network card in flux.
Note: This does not happen with 2008. Sysprepped OSes successfully get customized. It seems to be something new with 2012. I think this may be due to changes in the Sysprep process in 2012 vs. 2008.
At any rate, as per the advice above, I will retry with disabling/uninstalling the NIC entirely to see if that helps.
FYI I currently have a support ticket in with VMware with my findings and they have been able to replicate the issue themselves. They stated they will most likely have to work with MS for a resolution.