Is there any chance this was an upgrade using the Step-up upgrade bid? I'm thinking that it's possible that these upgrades book into a fare class that isn't recognized (e.g. R class or similar), and partner earnings don't recognize it as an eligible fare.
I had domestic 3 flights in recent weeks in SAA, all originally booked in V class which should have earned at least 50% mileage:
Flight 1 - V class, paid Step-up upgrade - no mileage posted
Flight 2 - V class, single cabin - posted as it should
Flight 3 - V class, paid Step-up upgrade - no mileage posted
I'd credited to AC and spouse credited to UA. I'd expect for paid upgrades that you'd at least get the mileage from the original fare basis, but the upgraded segments didn't credit on either AC or UA.
Also, both of the upgraded segments for me showed "First Class" on the boarding pass, and were printed by SAA agents.