10.12.4 has some new features that can cause trouble with your build. One is that you need a newer copy of Clover to boot with (I used r4049). The other is that I had a lot of trouble with Ethernet drivers that had worked fine with 10.12.3.
Fortunately though, I was on insanelymac, and Mieze had posted a new version of his IntelMausi Ethernet driver, and it worked!!
Version is: IntelMausiEthernet-V2.3.0d0
Congratulations for fixing the issue but I can definitely rule out, that it was the new driver version which solved the problem. Neither Apple changed the driver interface in 10.12.4, nor did I change support for the I218 in the new version and I can confirm that version 2.2.1 is working perfectly with the I218. Version 2.3.0d0 of IntelMausiEthernet only adds support for Kabylake and jumbo frames, that's all. You probably had a messed up system (system caches, network configuration or something like that) which has been fixed by the installation procedure.