Eric:

The only PCI error I can find in the journal while booting dom0 is:
"dom0 libvirtd[2788]: 2018-09-20 19:01:02.052+0000: 2829: error :
virPCIGetHeaderType:3129 : internal error: Unknown PCI header type '127'"

"qvm-pci list" does not show that NIC (understandable) however it is in the
Qubes manager device selection list as:
"dom0:01_00.0   Ethernet controller: Realtek Semiconductor Co., Ltd.
RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev ff)"
The NIC that is OK (device dom0:03_00.0) is the same except it has "(rev 07)" at
the end.

Your troubleshooting steps are sound. Test that "rev ff" device under a different OS to rule out a hardware problem, and in dom0 do a "sudo lspci -vvv" and compare the two Realtek entries against each other. Check to see if there's a firmware update for your system, sometime those include NIC firmware.

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