Does your itinerary include any Delta flights and/or travel to North America?
The reason why I ask, is that I have never had a single AF flight properly post to my Skymiles account when it was an AF ticket that had solely intra-Europe flights on it. Tickets that are a mix of AF/DL transatlantic flights and AF flights within Europe post ok. But any ticket that is solely composed of AF flights within Europe will not post properly - I've had dozens of tickets where I've had to request for the mileage credit to be done manually.