Was hoping for somebody else to try this as well, since I can't test for 20 hours. This is what I did today, which seems to have reproduced the claims people are making about not getting commendations:
1. Claimed rewards on existing rep projects to ensure I'm outside the cooldown.
2. Pick up Allied Zone daily, but don't complete it.
3. Cross into the Contested Zone, pick up that daily, but don't complete it.
4. Beam down to the battle zone, complete a run, get all normal rewards but no commendation.
5. Complete The Breach on normal in a pug, receive all rewards except commendation.
6. Return to Allied Zone, complete dailiy, receive commendation.
This leads me to believe that having an eligible but incomplete source of commendations in your journal prevents other sources from awarding them, forcing you to backtrack to the first mission you picked up.
I'm going to try a variation tomorrow to make sure this wasn't a fluke, but with the cooldown I'm posting here early so others players/devs can investigate.
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