When running Centos, does lspci -vvv give the same unusual output for that problem device? Don't know what else to suggest; I have a Realtek dual port RTL8111/8168/8411 PCI Express card in one of my systems and it works fine under Qubes 4.0.

No "lspci -vvv" outputs a complete description of both controllers as expected and 01:00.0's first line ends with "(rev 07)" as it should.

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