I was having this same issue and it was related to the "EVC mode" of the ESX cluster. I changed the VMware EVC mode to Intel "Nehalem" Generation and finally was able to see the interfaces. One thing that helped me find this solution was running "show controller dpa log stdout" which showed the log message "binary requires CPU with SSE4.2 extensions" repeating. I was not seeing the "Cisco IOS-XRv 9000 Centralized Line Card" until I changed the EVC mode on the ESX cluster to Nehalem.
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