I would agree that normally the earning rules on the operator website are just that - earnings when crediting to the operators FF programme. To be ignored when crediting to another *A programme.
When crediting to another program, eg UA, their crediting rules should be used. And if the flight was booked in U, it makes no sense to me that it would be credited as an E flight.
However, what is possible is that the fare code for the trip is not the same as the fare code for the individual flight segments. Did you happen to verify that all of them were U class?