I had a similar issue with Avianca but the miles were credited a few weeks after as i got in contact with A3. A3 is correct. Once you sent them your boarding pass etc then they contact the airline (in your case swiss) and they have to credit the miles.
I used the upgrade bid system with Avianca and my ticket changed from O to I and i could not get the miles. Once i got in contact with A3 i sent them all the details and a few weeks after i received the miles.