I flew from Paraguay to Peru a year or so ago. Operated by TA, marketed by AV. Flight was on a booking issued by KLM, contained a bunch of Skyteam sectors - and this one Star flight (Crazy TA!). During check in I specifically asked my M+B card to be put in the system as the rest of the itinerary was crediting to my Flying Blue account.

Well, you guessed it; it did not post. Then the online tool was just hanging in a 'waiting for approval by AV' kind of state for months. Eventually I contacted them by email, sent my boarding pass showing the A3 FF number, a few back-and-forth emails, and about a month later it was credited. I suspect they just manually added the miles, as contacting AV did not seem to work out well.

I'm not sure if these problems came forth out of the fact that the main booking had a Flying Blue FF number attached to it, or something else. Let us know if and how you get this resolved