I think the did not use to check for the class specifically before nor reject if you are not in the same class as ticketed.

What I suspect is that the new SW forgot to test the case for operational upgrade or maybe the agent did something a little non-standard to get the flight out. When I did a cert upgrade, the miles posted fine. I spent 3 calls and about 2 hours chasing this up beginning of August and the best they can tell me is that it was rejected since I was not found travelling in the class of my ticket. Yup, I was not in Y but sitting in front since they oversold the flight.