Last week I flew MSP-CDG-MAN, Delta ticketed, AF operated. My boarding passes, printed at MSP, all had my SM number. I received the miles about two days after the flights.
My itinerary on delta.com initially listed both the flights by their Delta code share numbers. After I used miles to upgrade from PE to Business on the first flight the flight number was listed by the AF number. I have no idea whether that is relevant to the OP's issue.