The problem i'm seeing is that the difficulty is getting set for both cards at the same level, and it's making one card get barely any submissions. I'm also getting Stratum connection interrupted.
I would normally think that your assumption (diff level) would be correct, but it was reporting accurately for my three cards (one being ~30% faster than the other two), so I'm not sure how they have it set up - I'm actually pretty sure that the server sees all three connections, despite there being only one username. You could try setting up a different password for each instance, or, like was said earlier (probably was you), set up a different wallet address for each miner.
As far as the stratum interruption, I did see that a few times while I was running in there, but a
very few. Not sure what might be causing this.